Starting phenix.real_space_refine on Fri Jul 3 02:23:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7khf_22879/07_2026/7khf_22879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7khf_22879/07_2026/7khf_22879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7khf_22879/07_2026/7khf_22879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7khf_22879/07_2026/7khf_22879.map" model { file = "/net/cci-nas-00/data/ceres_data/7khf_22879/07_2026/7khf_22879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7khf_22879/07_2026/7khf_22879.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7khf_22879/07_2026/7khf_22879.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7khf_22879/07_2026/7khf_22879.cif" } resolution = 3.54 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= -0.003 sd= 0.081 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 38 5.16 5 C 7283 2.51 5 N 1924 2.21 5 O 2314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11559 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3250 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 396} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1607 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain: "A" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3253 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 396} Chain: "B" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1607 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain: "D" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 851 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "C" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 851 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.08, per 1000 atoms: 0.18 Number of scatterers: 11559 At special positions: 0 Unit cell: (106.134, 137.541, 132.126, 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 38 16.00 O 2314 8.00 N 1924 7.00 C 7283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 251 " - pdb=" SG CYS H 302 " distance=2.03 Simple disulfide: pdb=" SG CYS H 339 " - pdb=" SG CYS B 213 " distance=2.71 Simple disulfide: pdb=" SG CYS H 352 " - pdb=" SG CYS H 408 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 408 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 242 " - pdb=" SG CYS D 264 " distance=2.03 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 264 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 501 " - " ASN A 207 " " NAG E 1 " - " ASN H 186 " " NAG F 1 " - " ASN H 246 " " NAG G 1 " - " ASN A 186 " " NAG H 501 " - " ASN H 207 " " NAG I 1 " - " ASN A 246 " Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 420.1 milliseconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 31 sheets defined 15.0% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'H' and resid 63 through 69 removed outlier: 3.814A pdb=" N LYS H 66 " --> pdb=" O PRO H 63 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER H 67 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU H 69 " --> pdb=" O LYS H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 197 removed outlier: 3.749A pdb=" N TYR H 196 " --> pdb=" O SER H 193 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY H 197 " --> pdb=" O ARG H 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 193 through 197' Processing helix chain 'H' and resid 413 through 416 Processing helix chain 'L' and resid 25 through 29 removed outlier: 3.632A pdb=" N ALA L 28 " --> pdb=" O ASP L 25 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG L 29 " --> pdb=" O SER L 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 25 through 29' Processing helix chain 'L' and resid 123 through 129 removed outlier: 4.050A pdb=" N LEU L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA L 129 " --> pdb=" O GLU L 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 123 through 129' Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.562A pdb=" N LYS L 188 " --> pdb=" O PRO L 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 193 through 197 removed outlier: 4.044A pdb=" N GLY A 197 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 404 removed outlier: 4.035A pdb=" N GLY A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.596A pdb=" N HIS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 205 removed outlier: 3.819A pdb=" N ALA D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 removed outlier: 3.801A pdb=" N GLU D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 237 Processing helix chain 'D' and resid 238 through 242 Processing helix chain 'D' and resid 261 through 272 Processing helix chain 'D' and resid 282 through 303 Processing helix chain 'C' and resid 187 through 205 removed outlier: 4.052A pdb=" N ALA C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 193 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.637A pdb=" N GLU C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 217 removed outlier: 4.018A pdb=" N SER C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 217' Processing helix chain 'C' and resid 225 through 237 removed outlier: 4.256A pdb=" N ILE C 229 " --> pdb=" O ASP C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 261 through 272 removed outlier: 3.551A pdb=" N SER C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 303 removed outlier: 3.622A pdb=" N GLY C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 299 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'H' and resid 18 through 22 removed outlier: 3.708A pdb=" N ARG H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.201A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY H 35 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ASN H 109 " --> pdb=" O PHE H 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 132 through 136 removed outlier: 4.049A pdb=" N GLN H 136 " --> pdb=" O THR H 148 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR H 148 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER H 183 " --> pdb=" O SER H 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 140 through 141 removed outlier: 6.805A pdb=" N VAL H 141 " --> pdb=" O ALA H 224 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU H 313 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE H 223 " --> pdb=" O LEU H 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 140 through 141 removed outlier: 6.805A pdb=" N VAL H 141 " --> pdb=" O ALA H 224 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY H 198 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL H 161 " --> pdb=" O TYR H 203 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN H 172 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY H 175 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASN C 276 " --> pdb=" O GLY H 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 231 through 235 removed outlier: 6.107A pdb=" N VAL H 247 " --> pdb=" O MET H 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 240 through 241 removed outlier: 3.752A pdb=" N TYR H 300 " --> pdb=" O LEU H 320 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 333 through 336 removed outlier: 3.686A pdb=" N GLY H 351 " --> pdb=" O LEU H 336 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP H 356 " --> pdb=" O TYR H 388 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR H 388 " --> pdb=" O ASP H 356 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER H 391 " --> pdb=" O PRO H 379 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL H 393 " --> pdb=" O THR H 377 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N THR H 377 " --> pdb=" O VAL H 393 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 363 through 366 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.541A pdb=" N SER L 62 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 44 through 48 removed outlier: 6.674A pdb=" N TRP L 34 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.752A pdb=" N SER L 139 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR L 174 " --> pdb=" O ASP L 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 155 through 156 removed outlier: 3.554A pdb=" N LYS L 206 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.544A pdb=" N THR A 119 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 95 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 51 " --> pdb=" O TRP A 38 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG A 40 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N TRP A 49 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.544A pdb=" N THR A 119 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 95 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS A 97 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP A 115 " --> pdb=" O CYS A 97 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS A 99 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 113 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 132 through 136 removed outlier: 3.926A pdb=" N THR A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 140 through 141 removed outlier: 3.620A pdb=" N VAL A 161 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 159 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 172 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 231 through 235 removed outlier: 5.711A pdb=" N VAL A 247 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 284 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 240 through 242 removed outlier: 3.711A pdb=" N SER A 325 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 300 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 274 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 332 through 336 removed outlier: 6.145A pdb=" N TYR A 388 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 332 through 336 removed outlier: 6.145A pdb=" N TYR A 388 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 362 through 366 Processing sheet with id=AC9, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.655A pdb=" N TYR B 85 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP B 34 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.655A pdb=" N TYR B 85 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AD3, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.388A pdb=" N TYR B 174 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 155 through 156 436 hydrogen bonds defined for protein. 1086 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: 1.61 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1887 1.30 - 1.43: 3082 1.43 - 1.56: 6816 1.56 - 1.69: 0 1.69 - 1.82: 44 Bond restraints: 11829 Sorted by residual: bond pdb=" CA CYS H 352 " pdb=" C CYS H 352 " ideal model delta sigma weight residual 1.522 1.395 0.126 1.21e-02 6.83e+03 1.08e+02 bond pdb=" C PRO A 361 " pdb=" O PRO A 361 " ideal model delta sigma weight residual 1.235 1.178 0.057 7.90e-03 1.60e+04 5.16e+01 bond pdb=" C PRO A 359 " pdb=" O PRO A 359 " ideal model delta sigma weight residual 1.233 1.169 0.064 1.10e-02 8.26e+03 3.39e+01 bond pdb=" N CYS H 352 " pdb=" CA CYS H 352 " ideal model delta sigma weight residual 1.454 1.386 0.069 1.27e-02 6.20e+03 2.92e+01 bond pdb=" CA SER H 389 " pdb=" CB SER H 389 " ideal model delta sigma weight residual 1.535 1.433 0.102 1.90e-02 2.77e+03 2.88e+01 ... (remaining 11824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 15669 2.85 - 5.71: 402 5.71 - 8.56: 43 8.56 - 11.41: 10 11.41 - 14.26: 2 Bond angle restraints: 16126 Sorted by residual: angle pdb=" C PRO A 331 " pdb=" CA PRO A 331 " pdb=" CB PRO A 331 " ideal model delta sigma weight residual 111.23 96.97 14.26 1.28e+00 6.10e-01 1.24e+02 angle pdb=" C PRO A 361 " pdb=" CA PRO A 361 " pdb=" CB PRO A 361 " ideal model delta sigma weight residual 111.87 103.74 8.13 8.40e-01 1.42e+00 9.37e+01 angle pdb=" C THR A 372 " pdb=" CA THR A 372 " pdb=" CB THR A 372 " ideal model delta sigma weight residual 110.81 122.95 -12.14 1.73e+00 3.34e-01 4.93e+01 angle pdb=" CA PRO H 338 " pdb=" C PRO H 338 " pdb=" O PRO H 338 " ideal model delta sigma weight residual 119.34 109.12 10.22 1.47e+00 4.63e-01 4.84e+01 angle pdb=" C PRO H 335 " pdb=" CA PRO H 335 " pdb=" CB PRO H 335 " ideal model delta sigma weight residual 110.98 102.28 8.70 1.31e+00 5.83e-01 4.42e+01 ... (remaining 16121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6435 17.95 - 35.90: 524 35.90 - 53.86: 74 53.86 - 71.81: 9 71.81 - 89.76: 5 Dihedral angle restraints: 7047 sinusoidal: 2681 harmonic: 4366 Sorted by residual: dihedral pdb=" C PRO A 331 " pdb=" N PRO A 331 " pdb=" CA PRO A 331 " pdb=" CB PRO A 331 " ideal model delta harmonic sigma weight residual -120.70 -102.15 -18.55 0 2.50e+00 1.60e-01 5.51e+01 dihedral pdb=" C PRO A 359 " pdb=" N PRO A 359 " pdb=" CA PRO A 359 " pdb=" CB PRO A 359 " ideal model delta harmonic sigma weight residual -120.70 -105.80 -14.90 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" CB CYS A 251 " pdb=" SG CYS A 251 " pdb=" SG CYS A 302 " pdb=" CB CYS A 302 " ideal model delta sinusoidal sigma weight residual 93.00 143.82 -50.82 1 1.00e+01 1.00e-02 3.54e+01 ... (remaining 7044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1796 0.154 - 0.308: 58 0.308 - 0.462: 9 0.462 - 0.616: 0 0.616 - 0.770: 2 Chirality restraints: 1865 Sorted by residual: chirality pdb=" CA CYS H 352 " pdb=" N CYS H 352 " pdb=" C CYS H 352 " pdb=" CB CYS H 352 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 246 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA THR A 372 " pdb=" N THR A 372 " pdb=" C THR A 372 " pdb=" CB THR A 372 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 1862 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO H 338 " 0.028 2.00e-02 2.50e+03 6.20e-02 3.84e+01 pdb=" C PRO H 338 " -0.107 2.00e-02 2.50e+03 pdb=" O PRO H 338 " 0.040 2.00e-02 2.50e+03 pdb=" N CYS H 339 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 246 " 0.001 2.00e-02 2.50e+03 4.04e-02 2.04e+01 pdb=" CG ASN A 246 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 246 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN A 246 " 0.050 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 335 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C PRO H 335 " 0.053 2.00e-02 2.50e+03 pdb=" O PRO H 335 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU H 336 " -0.018 2.00e-02 2.50e+03 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 673 2.72 - 3.27: 11207 3.27 - 3.81: 16916 3.81 - 4.36: 19939 4.36 - 4.90: 36296 Nonbonded interactions: 85031 Sorted by model distance: nonbonded pdb=" OE2 GLU A 6 " pdb=" N GLY A 118 " model vdw 2.179 3.120 nonbonded pdb=" NZ LYS B 168 " pdb=" OD1 ASN B 172 " model vdw 2.197 3.120 nonbonded pdb=" NH2 ARG H 68 " pdb=" OD2 ASP H 91 " model vdw 2.219 3.120 nonbonded pdb=" NZ LYS H 130 " pdb=" OG1 THR A 70 " model vdw 2.246 3.120 nonbonded pdb=" OE2 GLU H 265 " pdb=" NH2 ARG H 301 " model vdw 2.318 3.120 ... (remaining 85026 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 1 through 207 or (resid 208 and (name N or name CA or name \ C or name O or name CB )) or resid 209 through 501)) selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 9.540 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 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 : 0.010 0.674 11854 Z= 0.556 Angle : 1.000 19.369 16186 Z= 0.630 Chirality : 0.069 0.770 1865 Planarity : 0.005 0.062 2064 Dihedral : 12.720 89.760 4214 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.65 % Favored : 94.22 % Rotamer: Outliers : 0.94 % Allowed : 1.57 % Favored : 97.49 % Cbeta Deviations : 0.50 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.23), residues: 1504 helix: 0.24 (0.40), residues: 178 sheet: 0.32 (0.23), residues: 553 loop : -1.03 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 341 TYR 0.040 0.002 TYR A 357 PHE 0.035 0.002 PHE A 358 TRP 0.013 0.001 TRP H 256 HIS 0.005 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00772 / 0.46 (11829) covalent geometry : angle 0.97674 / 0.62 (16126) SS BOND : bond 0.17422 / 8.72 ( 15) SS BOND : angle 3.76488 / 2.59 ( 30) hydrogen bonds : bond 0.26211 / 17.14 ( 414) hydrogen bonds : angle 9.30235 / 6.23 ( 1086) link_BETA1-4 : bond 0.01065 / 0.54 ( 4) link_BETA1-4 : angle 2.62473 / 1.66 ( 12) link_NAG-ASN : bond 0.00443 / 0.15 ( 6) link_NAG-ASN : angle 4.03690 / 2.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 154 ASP cc_start: 0.7848 (t0) cc_final: 0.7599 (t0) REVERT: H 256 TRP cc_start: 0.7843 (t60) cc_final: 0.7637 (t-100) REVERT: H 257 MET cc_start: 0.7819 (mpp) cc_final: 0.7349 (mpp) REVERT: L 200 GLU cc_start: 0.7704 (pp20) cc_final: 0.7417 (pp20) REVERT: A 336 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9046 (pp) REVERT: A 341 ARG cc_start: 0.5812 (OUTLIER) cc_final: 0.5018 (tpp-160) REVERT: A 357 TYR cc_start: 0.8367 (p90) cc_final: 0.7530 (p90) REVERT: B 130 ASN cc_start: 0.8460 (m-40) cc_final: 0.7908 (t0) REVERT: D 288 GLN cc_start: 0.8516 (tp40) cc_final: 0.8274 (tp40) REVERT: D 294 ILE cc_start: 0.8587 (mm) cc_final: 0.8334 (tt) REVERT: C 230 THR cc_start: 0.9337 (m) cc_final: 0.9021 (p) REVERT: C 290 ASP cc_start: 0.7646 (m-30) cc_final: 0.7142 (m-30) outliers start: 12 outliers final: 4 residues processed: 186 average time/residue: 0.0871 time to fit residues: 23.8635 Evaluate side-chains 145 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.0570 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.081981 restraints weight = 22458.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.085238 restraints weight = 11041.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.087285 restraints weight = 7302.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.088624 restraints weight = 5644.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.089501 restraints weight = 4766.166| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11854 Z= 0.184 Angle : 0.671 7.264 16186 Z= 0.343 Chirality : 0.045 0.235 1865 Planarity : 0.005 0.042 2064 Dihedral : 5.396 54.794 1641 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.94 % Allowed : 8.22 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.23), residues: 1504 helix: 0.14 (0.39), residues: 186 sheet: 0.42 (0.23), residues: 557 loop : -0.99 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 341 TYR 0.013 0.001 TYR A 228 PHE 0.030 0.001 PHE A 358 TRP 0.008 0.001 TRP A 49 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (11829) covalent geometry : angle 0.66427 / 0.34 (16126) SS BOND : bond 0.00277 / 0.15 ( 15) SS BOND : angle 0.67101 / 0.43 ( 30) hydrogen bonds : bond 0.04816 / 3.20 ( 414) hydrogen bonds : angle 6.66172 / 4.50 ( 1086) link_BETA1-4 : bond 0.00691 / 0.35 ( 4) link_BETA1-4 : angle 2.39528 / 1.53 ( 12) link_NAG-ASN : bond 0.00169 / 0.08 ( 6) link_NAG-ASN : angle 2.30415 / 1.26 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: H 256 TRP cc_start: 0.8103 (t60) cc_final: 0.7811 (t-100) REVERT: H 257 MET cc_start: 0.8006 (mpp) cc_final: 0.7763 (mpp) REVERT: L 130 ASN cc_start: 0.8929 (t0) cc_final: 0.8679 (t0) REVERT: A 336 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8601 (pp) REVERT: A 409 ASN cc_start: 0.8572 (m-40) cc_final: 0.8342 (m-40) REVERT: B 130 ASN cc_start: 0.8511 (m-40) cc_final: 0.7878 (t0) REVERT: B 168 LYS cc_start: 0.8494 (tptt) cc_final: 0.8254 (mmmt) REVERT: D 288 GLN cc_start: 0.8268 (tp40) cc_final: 0.7941 (tp40) REVERT: D 294 ILE cc_start: 0.8708 (mm) cc_final: 0.8365 (tt) outliers start: 12 outliers final: 8 residues processed: 168 average time/residue: 0.0909 time to fit residues: 22.4082 Evaluate side-chains 151 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 267 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 146 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.081628 restraints weight = 22557.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.084878 restraints weight = 11064.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.086935 restraints weight = 7306.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.088264 restraints weight = 5654.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.089045 restraints weight = 4781.805| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11854 Z= 0.186 Angle : 0.640 7.444 16186 Z= 0.321 Chirality : 0.044 0.242 1865 Planarity : 0.004 0.039 2064 Dihedral : 5.188 52.794 1637 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.04 % Allowed : 10.42 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.23), residues: 1504 helix: 0.09 (0.39), residues: 187 sheet: 0.35 (0.23), residues: 579 loop : -0.97 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 191 TYR 0.011 0.001 TYR B 48 PHE 0.024 0.001 PHE H 334 TRP 0.010 0.001 TRP L 187 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (11829) covalent geometry : angle 0.63182 / 0.32 (16126) SS BOND : bond 0.00450 / 0.29 ( 15) SS BOND : angle 0.68590 / 0.45 ( 30) hydrogen bonds : bond 0.03926 / 2.64 ( 414) hydrogen bonds : angle 6.03019 / 4.06 ( 1086) link_BETA1-4 : bond 0.00692 / 0.35 ( 4) link_BETA1-4 : angle 2.25735 / 1.43 ( 12) link_NAG-ASN : bond 0.00237 / 0.09 ( 6) link_NAG-ASN : angle 2.47407 / 1.35 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: H 256 TRP cc_start: 0.8143 (t60) cc_final: 0.7534 (t-100) REVERT: H 420 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: L 130 ASN cc_start: 0.9007 (t0) cc_final: 0.8708 (t0) REVERT: A 336 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8577 (pp) REVERT: A 409 ASN cc_start: 0.8661 (m-40) cc_final: 0.8358 (m-40) REVERT: B 78 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8373 (mp10) REVERT: B 130 ASN cc_start: 0.8545 (m-40) cc_final: 0.7933 (t0) REVERT: B 140 ASP cc_start: 0.8333 (m-30) cc_final: 0.8093 (m-30) REVERT: B 168 LYS cc_start: 0.8496 (tptt) cc_final: 0.8047 (tptt) REVERT: D 288 GLN cc_start: 0.8280 (tp40) cc_final: 0.7956 (tp40) REVERT: C 290 ASP cc_start: 0.7963 (m-30) cc_final: 0.7333 (m-30) outliers start: 26 outliers final: 20 residues processed: 165 average time/residue: 0.1036 time to fit residues: 25.2317 Evaluate side-chains 163 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 278 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 75 optimal weight: 5.9990 chunk 80 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.105329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.081032 restraints weight = 22421.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.084178 restraints weight = 10991.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.086169 restraints weight = 7247.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.087377 restraints weight = 5616.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.088241 restraints weight = 4777.834| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11854 Z= 0.199 Angle : 0.635 7.511 16186 Z= 0.318 Chirality : 0.044 0.243 1865 Planarity : 0.004 0.038 2064 Dihedral : 5.140 51.877 1637 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.43 % Allowed : 11.82 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.23), residues: 1504 helix: 0.14 (0.39), residues: 187 sheet: 0.43 (0.23), residues: 558 loop : -1.02 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.010 0.001 TYR B 48 PHE 0.021 0.002 PHE H 334 TRP 0.008 0.001 TRP A 49 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (11829) covalent geometry : angle 0.62709 / 0.32 (16126) SS BOND : bond 0.00289 / 0.18 ( 15) SS BOND : angle 0.62309 / 0.40 ( 30) hydrogen bonds : bond 0.03687 / 2.47 ( 414) hydrogen bonds : angle 5.74626 / 3.86 ( 1086) link_BETA1-4 : bond 0.00713 / 0.36 ( 4) link_BETA1-4 : angle 2.03305 / 1.28 ( 12) link_NAG-ASN : bond 0.00236 / 0.09 ( 6) link_NAG-ASN : angle 2.58443 / 1.40 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 256 TRP cc_start: 0.7976 (t60) cc_final: 0.7699 (t60) REVERT: H 257 MET cc_start: 0.7849 (mpp) cc_final: 0.7457 (mpp) REVERT: H 336 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8814 (pp) REVERT: H 420 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7528 (m-30) REVERT: L 35 TYR cc_start: 0.9044 (m-80) cc_final: 0.8736 (m-80) REVERT: L 130 ASN cc_start: 0.9025 (t0) cc_final: 0.8710 (t0) REVERT: A 409 ASN cc_start: 0.8710 (m-40) cc_final: 0.8404 (m-40) REVERT: B 78 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8351 (mp10) REVERT: B 130 ASN cc_start: 0.8594 (m-40) cc_final: 0.7939 (t0) REVERT: B 140 ASP cc_start: 0.8374 (m-30) cc_final: 0.8120 (m-30) REVERT: B 168 LYS cc_start: 0.8505 (tptt) cc_final: 0.8133 (tptt) REVERT: D 279 ASP cc_start: 0.8228 (p0) cc_final: 0.8002 (p0) REVERT: D 288 GLN cc_start: 0.8369 (tp40) cc_final: 0.8031 (tp40) REVERT: C 290 ASP cc_start: 0.7905 (m-30) cc_final: 0.7307 (m-30) outliers start: 31 outliers final: 22 residues processed: 163 average time/residue: 0.1047 time to fit residues: 25.2236 Evaluate side-chains 162 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 267 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 115 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.106143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.081804 restraints weight = 22232.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.084981 restraints weight = 10879.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.087018 restraints weight = 7163.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.088325 restraints weight = 5522.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.089092 restraints weight = 4652.076| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11854 Z= 0.153 Angle : 0.603 7.111 16186 Z= 0.300 Chirality : 0.043 0.245 1865 Planarity : 0.004 0.037 2064 Dihedral : 4.947 40.654 1637 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.66 % Allowed : 12.92 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.23), residues: 1504 helix: 0.12 (0.39), residues: 187 sheet: 0.50 (0.23), residues: 558 loop : -0.98 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.010 0.001 TYR B 48 PHE 0.016 0.001 PHE H 334 TRP 0.007 0.001 TRP A 49 HIS 0.003 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (11829) covalent geometry : angle 0.59524 / 0.30 (16126) SS BOND : bond 0.00252 / 0.16 ( 15) SS BOND : angle 0.52319 / 0.34 ( 30) hydrogen bonds : bond 0.03290 / 2.21 ( 414) hydrogen bonds : angle 5.53859 / 3.73 ( 1086) link_BETA1-4 : bond 0.00802 / 0.40 ( 4) link_BETA1-4 : angle 1.99200 / 1.25 ( 12) link_NAG-ASN : bond 0.00257 / 0.11 ( 6) link_NAG-ASN : angle 2.50197 / 1.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 257 MET cc_start: 0.7808 (mpp) cc_final: 0.7155 (mpp) REVERT: H 336 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8761 (pp) REVERT: H 420 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7437 (m-30) REVERT: L 35 TYR cc_start: 0.9012 (m-80) cc_final: 0.8768 (m-80) REVERT: L 130 ASN cc_start: 0.9025 (t0) cc_final: 0.8729 (t0) REVERT: A 409 ASN cc_start: 0.8705 (m-40) cc_final: 0.8458 (m-40) REVERT: B 78 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8311 (mp10) REVERT: B 130 ASN cc_start: 0.8603 (m-40) cc_final: 0.7951 (t0) REVERT: B 140 ASP cc_start: 0.8379 (m-30) cc_final: 0.8112 (m-30) REVERT: B 168 LYS cc_start: 0.8494 (tptt) cc_final: 0.8105 (tptt) REVERT: D 288 GLN cc_start: 0.8329 (tp40) cc_final: 0.7984 (tp40) REVERT: C 290 ASP cc_start: 0.7819 (m-30) cc_final: 0.7292 (m-30) outliers start: 34 outliers final: 23 residues processed: 165 average time/residue: 0.0990 time to fit residues: 24.2340 Evaluate side-chains 163 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 267 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 92 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 119 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.106557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.081624 restraints weight = 22440.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.084888 restraints weight = 11051.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.086966 restraints weight = 7297.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.088299 restraints weight = 5637.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.089138 restraints weight = 4761.942| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11854 Z= 0.157 Angle : 0.600 7.698 16186 Z= 0.299 Chirality : 0.043 0.249 1865 Planarity : 0.004 0.036 2064 Dihedral : 4.729 37.840 1635 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.27 % Allowed : 14.10 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.23), residues: 1504 helix: 0.24 (0.39), residues: 187 sheet: 0.51 (0.23), residues: 572 loop : -0.92 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.010 0.001 TYR B 48 PHE 0.014 0.001 PHE H 334 TRP 0.007 0.001 TRP A 49 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (11829) covalent geometry : angle 0.59317 / 0.30 (16126) SS BOND : bond 0.00236 / 0.15 ( 15) SS BOND : angle 0.51143 / 0.33 ( 30) hydrogen bonds : bond 0.03239 / 2.18 ( 414) hydrogen bonds : angle 5.37481 / 3.61 ( 1086) link_BETA1-4 : bond 0.00760 / 0.38 ( 4) link_BETA1-4 : angle 1.88961 / 1.19 ( 12) link_NAG-ASN : bond 0.00233 / 0.09 ( 6) link_NAG-ASN : angle 2.47129 / 1.34 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 257 MET cc_start: 0.7826 (mpp) cc_final: 0.7111 (mpp) REVERT: H 336 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8757 (pp) REVERT: H 420 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: L 130 ASN cc_start: 0.9052 (t0) cc_final: 0.8762 (t0) REVERT: A 409 ASN cc_start: 0.8706 (m-40) cc_final: 0.8345 (m-40) REVERT: B 78 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8275 (mp10) REVERT: B 130 ASN cc_start: 0.8614 (m-40) cc_final: 0.7952 (t0) REVERT: B 140 ASP cc_start: 0.8408 (m-30) cc_final: 0.8120 (m-30) REVERT: B 168 LYS cc_start: 0.8481 (tptt) cc_final: 0.8122 (tptt) REVERT: D 288 GLN cc_start: 0.8363 (tp40) cc_final: 0.8009 (tp40) REVERT: C 290 ASP cc_start: 0.7823 (m-30) cc_final: 0.7277 (m-30) outliers start: 29 outliers final: 23 residues processed: 164 average time/residue: 0.0882 time to fit residues: 21.4135 Evaluate side-chains 163 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 267 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 24 optimal weight: 4.9990 chunk 132 optimal weight: 0.0470 chunk 61 optimal weight: 3.9990 chunk 19 optimal weight: 0.0370 chunk 29 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.105266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.082066 restraints weight = 21292.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.085038 restraints weight = 10867.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.086959 restraints weight = 7278.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.088203 restraints weight = 5648.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.088953 restraints weight = 4781.149| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11854 Z= 0.155 Angle : 0.602 7.338 16186 Z= 0.299 Chirality : 0.043 0.247 1865 Planarity : 0.004 0.036 2064 Dihedral : 4.669 38.148 1635 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.58 % Allowed : 14.57 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.23), residues: 1504 helix: 0.15 (0.38), residues: 187 sheet: 0.54 (0.23), residues: 574 loop : -0.91 (0.24), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.016 0.001 TYR A 228 PHE 0.013 0.001 PHE H 334 TRP 0.008 0.001 TRP A 49 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (11829) covalent geometry : angle 0.59473 / 0.30 (16126) SS BOND : bond 0.00239 / 0.14 ( 15) SS BOND : angle 0.48839 / 0.31 ( 30) hydrogen bonds : bond 0.03189 / 2.14 ( 414) hydrogen bonds : angle 5.31431 / 3.57 ( 1086) link_BETA1-4 : bond 0.00769 / 0.39 ( 4) link_BETA1-4 : angle 1.85393 / 1.17 ( 12) link_NAG-ASN : bond 0.00249 / 0.10 ( 6) link_NAG-ASN : angle 2.45318 / 1.33 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 257 MET cc_start: 0.7816 (mpp) cc_final: 0.7151 (mpp) REVERT: H 336 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8897 (pp) REVERT: H 420 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7540 (m-30) REVERT: L 130 ASN cc_start: 0.8904 (t0) cc_final: 0.8634 (t0) REVERT: A 409 ASN cc_start: 0.8680 (m-40) cc_final: 0.8325 (m-40) REVERT: B 78 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8420 (mp10) REVERT: B 130 ASN cc_start: 0.8601 (m-40) cc_final: 0.8000 (t0) REVERT: B 140 ASP cc_start: 0.8382 (m-30) cc_final: 0.8124 (m-30) REVERT: B 168 LYS cc_start: 0.8361 (tptt) cc_final: 0.8092 (tptt) REVERT: D 288 GLN cc_start: 0.8510 (tp40) cc_final: 0.8189 (tp40) REVERT: C 231 THR cc_start: 0.8749 (p) cc_final: 0.8549 (t) REVERT: C 290 ASP cc_start: 0.7689 (m-30) cc_final: 0.7209 (m-30) outliers start: 33 outliers final: 27 residues processed: 160 average time/residue: 0.0928 time to fit residues: 22.1008 Evaluate side-chains 167 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 267 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 99 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 75 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.110282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.085232 restraints weight = 22825.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.089363 restraints weight = 11992.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.091573 restraints weight = 6972.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.091691 restraints weight = 5619.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.091847 restraints weight = 5261.583| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11854 Z= 0.135 Angle : 0.587 7.122 16186 Z= 0.291 Chirality : 0.043 0.249 1865 Planarity : 0.004 0.036 2064 Dihedral : 4.580 38.531 1634 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.66 % Allowed : 14.96 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.22), residues: 1504 helix: 0.20 (0.39), residues: 183 sheet: 0.60 (0.23), residues: 572 loop : -0.95 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.021 0.001 TYR C 223 PHE 0.014 0.001 PHE C 204 TRP 0.006 0.001 TRP A 49 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (11829) covalent geometry : angle 0.58033 / 0.29 (16126) SS BOND : bond 0.00222 / 0.14 ( 15) SS BOND : angle 0.47880 / 0.30 ( 30) hydrogen bonds : bond 0.03059 / 2.07 ( 414) hydrogen bonds : angle 5.24112 / 3.53 ( 1086) link_BETA1-4 : bond 0.00761 / 0.38 ( 4) link_BETA1-4 : angle 1.79890 / 1.13 ( 12) link_NAG-ASN : bond 0.00267 / 0.11 ( 6) link_NAG-ASN : angle 2.39627 / 1.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 257 MET cc_start: 0.7763 (mpp) cc_final: 0.7134 (mpp) REVERT: H 336 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8699 (pp) REVERT: H 420 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: L 130 ASN cc_start: 0.9080 (t0) cc_final: 0.8796 (t0) REVERT: L 200 GLU cc_start: 0.8166 (pp20) cc_final: 0.7887 (pp20) REVERT: A 409 ASN cc_start: 0.8699 (m-40) cc_final: 0.8323 (m-40) REVERT: B 78 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8269 (mp10) REVERT: B 130 ASN cc_start: 0.8618 (m-40) cc_final: 0.7942 (t0) REVERT: B 140 ASP cc_start: 0.8449 (m-30) cc_final: 0.8149 (m-30) REVERT: B 168 LYS cc_start: 0.8492 (tptt) cc_final: 0.8086 (tptt) REVERT: D 288 GLN cc_start: 0.8357 (tp40) cc_final: 0.8014 (tp40) REVERT: C 290 ASP cc_start: 0.7829 (m-30) cc_final: 0.7253 (m-30) outliers start: 34 outliers final: 25 residues processed: 171 average time/residue: 0.0908 time to fit residues: 23.2587 Evaluate side-chains 165 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 267 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 43 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.084689 restraints weight = 22629.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.087906 restraints weight = 11360.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.090006 restraints weight = 7595.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.091376 restraints weight = 5886.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.092179 restraints weight = 4981.443| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11854 Z= 0.148 Angle : 0.600 7.002 16186 Z= 0.298 Chirality : 0.043 0.251 1865 Planarity : 0.004 0.036 2064 Dihedral : 4.581 38.487 1634 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.90 % Allowed : 15.19 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.22), residues: 1504 helix: 0.14 (0.39), residues: 183 sheet: 0.61 (0.23), residues: 572 loop : -0.93 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.013 0.001 TYR C 223 PHE 0.017 0.001 PHE H 287 TRP 0.007 0.001 TRP A 49 HIS 0.004 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (11829) covalent geometry : angle 0.59325 / 0.30 (16126) SS BOND : bond 0.00227 / 0.14 ( 15) SS BOND : angle 0.48468 / 0.31 ( 30) hydrogen bonds : bond 0.03071 / 2.07 ( 414) hydrogen bonds : angle 5.20156 / 3.50 ( 1086) link_BETA1-4 : bond 0.00761 / 0.38 ( 4) link_BETA1-4 : angle 1.77400 / 1.12 ( 12) link_NAG-ASN : bond 0.00248 / 0.10 ( 6) link_NAG-ASN : angle 2.39193 / 1.29 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 257 MET cc_start: 0.7783 (mpp) cc_final: 0.7154 (mpp) REVERT: H 336 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8664 (pp) REVERT: H 420 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7489 (m-30) REVERT: L 130 ASN cc_start: 0.9059 (t0) cc_final: 0.8785 (t0) REVERT: L 200 GLU cc_start: 0.8171 (pp20) cc_final: 0.7683 (pp20) REVERT: A 409 ASN cc_start: 0.8701 (m-40) cc_final: 0.8326 (m-40) REVERT: B 78 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8312 (mp10) REVERT: B 140 ASP cc_start: 0.8456 (m-30) cc_final: 0.8157 (m-30) REVERT: B 168 LYS cc_start: 0.8467 (tptt) cc_final: 0.8081 (tptt) REVERT: D 229 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.8966 (tp) REVERT: D 288 GLN cc_start: 0.8329 (tp40) cc_final: 0.7983 (tp40) REVERT: C 290 ASP cc_start: 0.7832 (m-30) cc_final: 0.7242 (m-30) outliers start: 37 outliers final: 31 residues processed: 162 average time/residue: 0.0898 time to fit residues: 21.7950 Evaluate side-chains 169 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.109941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.084416 restraints weight = 22922.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.087581 restraints weight = 11538.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.089610 restraints weight = 7715.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.090841 restraints weight = 6006.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.091762 restraints weight = 5129.479| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11854 Z= 0.184 Angle : 0.622 6.910 16186 Z= 0.310 Chirality : 0.044 0.248 1865 Planarity : 0.004 0.036 2064 Dihedral : 4.634 38.115 1633 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.74 % Allowed : 15.58 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.22), residues: 1504 helix: 0.11 (0.38), residues: 189 sheet: 0.57 (0.23), residues: 572 loop : -0.97 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.022 0.001 TYR C 223 PHE 0.023 0.002 PHE H 287 TRP 0.009 0.001 TRP A 49 HIS 0.005 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.18 (11829) covalent geometry : angle 0.61542 / 0.31 (16126) SS BOND : bond 0.00242 / 0.15 ( 15) SS BOND : angle 0.54816 / 0.35 ( 30) hydrogen bonds : bond 0.03277 / 2.21 ( 414) hydrogen bonds : angle 5.28080 / 3.55 ( 1086) link_BETA1-4 : bond 0.00732 / 0.37 ( 4) link_BETA1-4 : angle 1.76487 / 1.11 ( 12) link_NAG-ASN : bond 0.00225 / 0.09 ( 6) link_NAG-ASN : angle 2.42941 / 1.31 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 257 MET cc_start: 0.7782 (mpp) cc_final: 0.7114 (mpp) REVERT: H 336 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8711 (pp) REVERT: H 420 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7522 (m-30) REVERT: L 130 ASN cc_start: 0.9066 (t0) cc_final: 0.8795 (t0) REVERT: A 409 ASN cc_start: 0.8721 (m-40) cc_final: 0.8317 (m-40) REVERT: B 78 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8339 (mp10) REVERT: B 140 ASP cc_start: 0.8480 (m-30) cc_final: 0.8178 (m-30) REVERT: B 168 LYS cc_start: 0.8499 (tptt) cc_final: 0.8221 (tptm) REVERT: D 229 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.8949 (tp) REVERT: D 288 GLN cc_start: 0.8355 (tp40) cc_final: 0.8005 (tp40) REVERT: C 290 ASP cc_start: 0.7802 (m-30) cc_final: 0.7194 (m-30) outliers start: 35 outliers final: 28 residues processed: 155 average time/residue: 0.0926 time to fit residues: 21.3296 Evaluate side-chains 164 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 58 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.086034 restraints weight = 22883.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.089274 restraints weight = 11484.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.091374 restraints weight = 7635.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.092699 restraints weight = 5897.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.093568 restraints weight = 5002.109| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11854 Z= 0.122 Angle : 0.597 6.917 16186 Z= 0.296 Chirality : 0.043 0.249 1865 Planarity : 0.004 0.035 2064 Dihedral : 4.515 38.785 1633 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.11 % Allowed : 16.21 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.22), residues: 1504 helix: 0.18 (0.39), residues: 183 sheet: 0.62 (0.23), residues: 572 loop : -0.88 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 29 TYR 0.009 0.001 TYR A 406 PHE 0.016 0.001 PHE C 204 TRP 0.006 0.001 TRP A 49 HIS 0.003 0.001 HIS H 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (11829) covalent geometry : angle 0.59018 / 0.29 (16126) SS BOND : bond 0.00213 / 0.13 ( 15) SS BOND : angle 0.46335 / 0.29 ( 30) hydrogen bonds : bond 0.02924 / 1.97 ( 414) hydrogen bonds : angle 5.17970 / 3.48 ( 1086) link_BETA1-4 : bond 0.00768 / 0.39 ( 4) link_BETA1-4 : angle 1.73988 / 1.10 ( 12) link_NAG-ASN : bond 0.00309 / 0.13 ( 6) link_NAG-ASN : angle 2.35294 / 1.27 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1915.07 seconds wall clock time: 33 minutes 57.69 seconds (2037.69 seconds total)