Starting phenix.real_space_refine on Wed Aug 27 00:10:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8st1_40754/08_2025/8st1_40754_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8st1_40754/08_2025/8st1_40754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8st1_40754/08_2025/8st1_40754_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8st1_40754/08_2025/8st1_40754_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8st1_40754/08_2025/8st1_40754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8st1_40754/08_2025/8st1_40754.map" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 S 120 5.16 5 Na 1 4.78 5 C 14329 2.51 5 N 3569 2.21 5 O 4067 1.98 5 H 21833 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43923 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 6195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 6195 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 355} Chain: "B" Number of atoms: 6195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 6195 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 355} Chain: "C" Number of atoms: 5978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5978 Classifications: {'peptide': 365} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 342} Chain breaks: 1 Chain: "D" Number of atoms: 6195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 6195 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 355} Chain: "E" Number of atoms: 5978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5978 Classifications: {'peptide': 365} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 342} Chain breaks: 1 Chain: "F" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "G" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3265 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "J" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "K" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3265 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Unusual residues: {' CA': 2, 'ACH': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {' CA': 1, 'ACH': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {' CA': 1, 'ACH': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.05, per 1000 atoms: 0.16 Number of scatterers: 43923 At special positions: 0 Unit cell: (137.953, 182.867, 146.508, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 S 120 16.00 Na 1 11.00 O 4067 8.00 N 3569 7.00 C 14329 6.00 H 21833 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 200 " distance=2.04 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 200 " distance=2.04 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 144 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 93 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 202 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 139 " - pdb=" SG CYS J 199 " distance=2.24 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 147 " - pdb=" SG CYS K 202 " 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 H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A 701 " - " ASN A 31 " " NAG A 702 " - " ASN A 148 " " NAG B 701 " - " ASN B 31 " " NAG B 702 " - " ASN B 148 " " NAG D 701 " - " ASN D 31 " " NAG D 702 " - " ASN D 148 " " NAG H 1 " - " ASN C 143 " " NAG I 1 " - " ASN E 143 " Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5220 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 39 sheets defined 30.3% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 8 through 19 Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 217 through 234 removed outlier: 4.403A pdb=" N ILE A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.745A pdb=" N LEU A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 4.360A pdb=" N VAL A 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 247 through 268 Processing helix chain 'A' and resid 278 through 306 Processing helix chain 'A' and resid 315 through 330 removed outlier: 5.551A pdb=" N VAL A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 341 through 382 Proline residue: A 379 - end of helix Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 75 through 80 removed outlier: 4.079A pdb=" N GLU B 80 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 224 Processing helix chain 'B' and resid 224 through 234 removed outlier: 3.868A pdb=" N LEU B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 241 removed outlier: 4.218A pdb=" N VAL B 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 247 through 268 Processing helix chain 'B' and resid 278 through 306 Processing helix chain 'B' and resid 315 through 324 removed outlier: 3.541A pdb=" N VAL B 321 " --> pdb=" O TRP B 317 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.848A pdb=" N ARG B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 382 Proline residue: B 379 - end of helix Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 65 through 68 removed outlier: 3.570A pdb=" N THR C 68 " --> pdb=" O TYR C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 65 through 68' Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.709A pdb=" N ASP C 75 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.313A pdb=" N ILE C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Proline residue: C 219 - end of helix removed outlier: 3.691A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 removed outlier: 4.209A pdb=" N VAL C 230 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 262 Processing helix chain 'C' and resid 270 through 298 Processing helix chain 'C' and resid 307 through 323 removed outlier: 5.793A pdb=" N LEU C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Proline residue: C 319 - end of helix Processing helix chain 'C' and resid 338 through 363 Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'D' and resid 9 through 19 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 217 through 234 removed outlier: 4.480A pdb=" N ILE D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.924A pdb=" N LEU D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 241 removed outlier: 4.003A pdb=" N TYR D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 246 removed outlier: 3.588A pdb=" N CYS D 245 " --> pdb=" O PRO D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 268 Processing helix chain 'D' and resid 278 through 306 Processing helix chain 'D' and resid 315 through 330 removed outlier: 5.543A pdb=" N VAL D 326 " --> pdb=" O PHE D 322 " (cutoff:3.500A) Proline residue: D 327 - end of helix Processing helix chain 'D' and resid 341 through 382 Proline residue: D 379 - end of helix Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 65 through 68 removed outlier: 3.644A pdb=" N THR E 68 " --> pdb=" O TYR E 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 65 through 68' Processing helix chain 'E' and resid 70 through 75 removed outlier: 4.163A pdb=" N ASP E 75 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 209 through 216 Processing helix chain 'E' and resid 216 through 226 removed outlier: 3.759A pdb=" N LEU E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 233 removed outlier: 4.381A pdb=" N VAL E 230 " --> pdb=" O ALA E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 Processing helix chain 'E' and resid 239 through 262 Processing helix chain 'E' and resid 270 through 298 Processing helix chain 'E' and resid 307 through 315 Processing helix chain 'E' and resid 316 through 322 removed outlier: 3.822A pdb=" N ALA E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 364 removed outlier: 3.556A pdb=" N CYS E 361 " --> pdb=" O PHE E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.965A pdb=" N LEU E 370 " --> pdb=" O ILE E 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 133 Processing helix chain 'F' and resid 188 through 192 Processing helix chain 'G' and resid 29 through 33 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 207 through 210 Processing helix chain 'J' and resid 84 through 88 Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 187 through 192 Processing helix chain 'K' and resid 29 through 33 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 88 removed outlier: 4.197A pdb=" N ARG A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY A 121 " --> pdb=" O ASP A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 88 removed outlier: 4.197A pdb=" N ARG A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY A 121 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N MET A 56 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP A 49 " --> pdb=" O MET A 56 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR A 58 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS A 68 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 37 " --> pdb=" O HIS A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 99 removed outlier: 4.238A pdb=" N SER A 155 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 189 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG A 214 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ILE A 185 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 87 removed outlier: 4.551A pdb=" N ARG B 122 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY B 121 " --> pdb=" O ASP B 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 87 removed outlier: 4.551A pdb=" N ARG B 122 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY B 121 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N MET B 56 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASP B 49 " --> pdb=" O MET B 56 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR B 58 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N HIS B 68 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B 37 " --> pdb=" O HIS B 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 99 removed outlier: 4.497A pdb=" N SER B 155 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLU B 202 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR B 197 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 204 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 189 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG B 214 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE B 185 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 79 through 83 removed outlier: 4.139A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP C 62 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 79 through 83 removed outlier: 4.139A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP C 62 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN C 55 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU C 42 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N TRP C 57 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA C 40 " --> pdb=" O TRP C 57 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR C 59 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N SER C 38 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLU C 61 " --> pdb=" O MET C 36 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N MET C 36 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N GLU C 63 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N GLN C 34 " --> pdb=" O GLU C 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.071A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE C 204 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.071A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 36 through 40 removed outlier: 6.208A pdb=" N VAL D 36 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL D 166 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL D 38 " --> pdb=" O VAL D 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 42 through 51 removed outlier: 6.697A pdb=" N ASN D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR D 58 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ASP D 49 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N MET D 56 " --> pdb=" O ASP D 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 65 through 73 removed outlier: 4.524A pdb=" N GLY D 121 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG D 122 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.293A pdb=" N SER D 155 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D 189 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG D 214 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ILE D 185 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 79 through 83 removed outlier: 4.255A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 79 through 83 removed outlier: 4.255A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE E 51 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER E 44 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N THR E 53 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LEU E 42 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASN E 55 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU E 63 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR E 32 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL E 31 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL E 161 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL E 33 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.099A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE E 204 " --> pdb=" O VAL E 181 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.099A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.526A pdb=" N THR F 7 " --> pdb=" O SER F 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.998A pdb=" N GLY F 89 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU F 42 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU F 51 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.998A pdb=" N GLY F 89 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR F 102 " --> pdb=" O GLN F 95 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 119 through 123 removed outlier: 3.594A pdb=" N VAL F 138 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER F 179 " --> pdb=" O THR F 169 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 149 through 152 removed outlier: 3.520A pdb=" N LYS F 212 " --> pdb=" O CYS F 199 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 154 through 155 Processing sheet with id=AC7, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.770A pdb=" N THR G 79 " --> pdb=" O ASP G 74 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.210A pdb=" N ILE G 35 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU G 51 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP G 37 " --> pdb=" O ILE G 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 127 through 130 removed outlier: 3.714A pdb=" N GLY G 151 " --> pdb=" O TYR G 182 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR G 182 " --> pdb=" O GLY G 151 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 127 through 130 removed outlier: 3.714A pdb=" N GLY G 151 " --> pdb=" O TYR G 182 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR G 182 " --> pdb=" O GLY G 151 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 158 through 161 removed outlier: 4.713A pdb=" N CYS G 202 " --> pdb=" O LYS G 215 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS G 215 " --> pdb=" O CYS G 202 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'J' and resid 58 through 59 removed outlier: 6.516A pdb=" N TRP J 40 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR J 54 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU J 38 " --> pdb=" O TYR J 54 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY J 89 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 119 through 123 Processing sheet with id=AD6, first strand: chain 'J' and resid 119 through 123 removed outlier: 6.153A pdb=" N TYR J 178 " --> pdb=" O ASN J 143 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER J 179 " --> pdb=" O THR J 169 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 158 through 159 removed outlier: 3.526A pdb=" N LYS J 212 " --> pdb=" O CYS J 199 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N HIS J 203 " --> pdb=" O SER J 208 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N SER J 208 " --> pdb=" O HIS J 203 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD9, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.332A pdb=" N ILE K 35 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU K 51 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TRP K 37 " --> pdb=" O ILE K 49 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 129 through 130 removed outlier: 3.861A pdb=" N LEU K 148 " --> pdb=" O TYR K 129 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY K 151 " --> pdb=" O TYR K 182 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR K 182 " --> pdb=" O GLY K 151 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 142 through 144 Processing sheet with id=AE3, first strand: chain 'K' and resid 160 through 161 removed outlier: 3.978A pdb=" N CYS K 202 " --> pdb=" O LYS K 215 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS K 215 " --> pdb=" O CYS K 202 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 2967 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: 11.64 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 21808 1.03 - 1.23: 847 1.23 - 1.43: 8955 1.43 - 1.63: 12717 1.63 - 1.83: 183 Bond restraints: 44510 Sorted by residual: bond pdb=" C ARG D 171 " pdb=" N VAL D 172 " ideal model delta sigma weight residual 1.334 1.368 -0.033 1.26e-02 6.30e+03 6.96e+00 bond pdb=" C ALA A 210 " pdb=" N PHE A 211 " ideal model delta sigma weight residual 1.331 1.363 -0.032 1.43e-02 4.89e+03 5.11e+00 bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ASP J 1 " pdb=" CA ASP J 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" CG ARG F 216 " pdb=" CD ARG F 216 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.30e+00 ... (remaining 44505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 79420 1.55 - 3.11: 910 3.11 - 4.66: 137 4.66 - 6.21: 12 6.21 - 7.77: 4 Bond angle restraints: 80483 Sorted by residual: angle pdb=" CB ARG F 216 " pdb=" CG ARG F 216 " pdb=" CD ARG F 216 " ideal model delta sigma weight residual 111.30 119.07 -7.77 2.30e+00 1.89e-01 1.14e+01 angle pdb=" CA ARG F 216 " pdb=" CB ARG F 216 " pdb=" CG ARG F 216 " ideal model delta sigma weight residual 114.10 119.77 -5.67 2.00e+00 2.50e-01 8.04e+00 angle pdb=" CG ARG F 216 " pdb=" CD ARG F 216 " pdb=" NE ARG F 216 " ideal model delta sigma weight residual 112.00 117.90 -5.90 2.20e+00 2.07e-01 7.19e+00 angle pdb=" C ASP C 193 " pdb=" N SER C 194 " pdb=" CA SER C 194 " ideal model delta sigma weight residual 121.54 126.51 -4.97 1.91e+00 2.74e-01 6.78e+00 angle pdb=" N SER K 179 " pdb=" CA SER K 179 " pdb=" C SER K 179 " ideal model delta sigma weight residual 112.93 109.95 2.98 1.33e+00 5.65e-01 5.03e+00 ... (remaining 80478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.90: 19860 21.90 - 43.80: 1176 43.80 - 65.70: 217 65.70 - 87.60: 49 87.60 - 109.50: 11 Dihedral angle restraints: 21313 sinusoidal: 11509 harmonic: 9804 Sorted by residual: dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 93 " pdb=" CB CYS J 93 " ideal model delta sinusoidal sigma weight residual -86.00 -169.54 83.54 1 1.00e+01 1.00e-02 8.52e+01 dihedral pdb=" CB CYS J 139 " pdb=" SG CYS J 139 " pdb=" SG CYS J 199 " pdb=" CB CYS J 199 " ideal model delta sinusoidal sigma weight residual 93.00 167.66 -74.66 1 1.00e+01 1.00e-02 7.06e+01 dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 149 " pdb=" CB CYS D 149 " ideal model delta sinusoidal sigma weight residual 93.00 33.27 59.73 1 1.00e+01 1.00e-02 4.76e+01 ... (remaining 21310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2980 0.053 - 0.106: 501 0.106 - 0.159: 108 0.159 - 0.212: 0 0.212 - 0.265: 2 Chirality restraints: 3591 Sorted by residual: chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE A 277 " pdb=" N ILE A 277 " pdb=" C ILE A 277 " pdb=" CB ILE A 277 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 ... (remaining 3588 not shown) Planarity restraints: 6379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 307 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO C 308 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 308 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 308 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 313 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C VAL E 313 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL E 313 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE E 314 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 213 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" C THR C 213 " 0.027 2.00e-02 2.50e+03 pdb=" O THR C 213 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE C 214 " -0.009 2.00e-02 2.50e+03 ... (remaining 6376 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.07: 538 2.07 - 2.70: 69923 2.70 - 3.33: 127328 3.33 - 3.97: 166521 3.97 - 4.60: 260256 Nonbonded interactions: 624566 Sorted by model distance: nonbonded pdb="HG13 VAL B 299 " pdb="HD13 LEU C 233 " model vdw 1.433 2.440 nonbonded pdb=" OE1 GLU F 86 " pdb=" H GLU F 86 " model vdw 1.446 2.450 nonbonded pdb=" OE1 GLU K 90 " pdb=" H GLU K 90 " model vdw 1.478 2.450 nonbonded pdb=" H ASP J 156 " pdb=" O SER J 196 " model vdw 1.545 2.450 nonbonded pdb=" OD2 ASP B 145 " pdb="HE21 GLN B 147 " model vdw 1.562 2.450 ... (remaining 624561 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 8 through 704) selection = chain 'B' selection = chain 'D' } ncs_group { reference = (chain 'C' and resid 1 through 372) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'H' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.230 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 38.040 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.005 0.212 22705 Z= 0.206 Angle : 0.533 8.869 31008 Z= 0.268 Chirality : 0.043 0.265 3591 Planarity : 0.003 0.056 3808 Dihedral : 15.268 109.502 8335 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.16), residues: 2705 helix: 1.67 (0.21), residues: 646 sheet: -0.66 (0.18), residues: 801 loop : -0.55 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 155 TYR 0.019 0.001 TYR K 182 PHE 0.010 0.001 PHE D 219 TRP 0.009 0.001 TRP F 101 HIS 0.003 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00444 (22677) covalent geometry : angle 0.52598 (30940) SS BOND : bond 0.05309 ( 16) SS BOND : angle 1.80044 ( 32) hydrogen bonds : bond 0.20543 ( 980) hydrogen bonds : angle 8.48723 ( 2967) link_BETA1-4 : bond 0.00287 ( 4) link_BETA1-4 : angle 1.80121 ( 12) link_NAG-ASN : bond 0.00288 ( 8) link_NAG-ASN : angle 1.99049 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 PHE cc_start: 0.7145 (m-80) cc_final: 0.6604 (m-10) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.3777 time to fit residues: 80.0730 Evaluate side-chains 131 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.102276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.069419 restraints weight = 123255.830| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.50 r_work: 0.2776 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22705 Z= 0.204 Angle : 0.555 6.968 31008 Z= 0.294 Chirality : 0.045 0.168 3591 Planarity : 0.004 0.046 3808 Dihedral : 6.675 70.700 3205 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.56 % Allowed : 10.97 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.16), residues: 2705 helix: 1.99 (0.20), residues: 651 sheet: -0.77 (0.18), residues: 808 loop : -0.61 (0.18), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 155 TYR 0.021 0.001 TYR K 182 PHE 0.012 0.001 PHE A 142 TRP 0.009 0.001 TRP F 101 HIS 0.004 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00474 (22677) covalent geometry : angle 0.54909 (30940) SS BOND : bond 0.00483 ( 16) SS BOND : angle 1.24987 ( 32) hydrogen bonds : bond 0.05338 ( 980) hydrogen bonds : angle 6.12267 ( 2967) link_BETA1-4 : bond 0.00345 ( 4) link_BETA1-4 : angle 2.35137 ( 12) link_NAG-ASN : bond 0.00307 ( 8) link_NAG-ASN : angle 1.99372 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 PHE cc_start: 0.7497 (m-80) cc_final: 0.6901 (m-10) REVERT: C 241 MET cc_start: 0.8523 (mmp) cc_final: 0.8230 (mmp) REVERT: D 169 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7544 (p-80) REVERT: E 155 ARG cc_start: 0.9024 (ttp80) cc_final: 0.8784 (ttp80) REVERT: J 82 ARG cc_start: 0.7235 (ttp80) cc_final: 0.6877 (ttp80) REVERT: J 110 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7513 (pt0) outliers start: 14 outliers final: 6 residues processed: 151 average time/residue: 0.3731 time to fit residues: 84.9453 Evaluate side-chains 142 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain J residue 110 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 240 optimal weight: 9.9990 chunk 153 optimal weight: 0.5980 chunk 236 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 118 optimal weight: 0.4980 chunk 237 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS E 371 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.103293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.070402 restraints weight = 122574.175| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.54 r_work: 0.2801 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22705 Z= 0.131 Angle : 0.489 5.114 31008 Z= 0.254 Chirality : 0.043 0.139 3591 Planarity : 0.004 0.039 3808 Dihedral : 5.023 43.065 3205 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.60 % Allowed : 11.49 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.16), residues: 2705 helix: 2.14 (0.20), residues: 663 sheet: -0.75 (0.18), residues: 804 loop : -0.61 (0.18), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 216 TYR 0.009 0.001 TYR E 275 PHE 0.009 0.001 PHE A 142 TRP 0.011 0.001 TRP G 161 HIS 0.004 0.001 HIS F 194 Details of bonding type rmsd covalent geometry : bond 0.00301 (22677) covalent geometry : angle 0.48437 (30940) SS BOND : bond 0.00459 ( 16) SS BOND : angle 1.03339 ( 32) hydrogen bonds : bond 0.04599 ( 980) hydrogen bonds : angle 5.49889 ( 2967) link_BETA1-4 : bond 0.00420 ( 4) link_BETA1-4 : angle 1.96939 ( 12) link_NAG-ASN : bond 0.00061 ( 8) link_NAG-ASN : angle 1.76020 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 371 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7423 (mt) REVERT: C 241 MET cc_start: 0.8317 (mmp) cc_final: 0.8057 (mmp) REVERT: D 169 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.7525 (p-80) REVERT: E 36 MET cc_start: 0.9224 (tmm) cc_final: 0.8962 (ttm) REVERT: E 155 ARG cc_start: 0.9014 (ttp80) cc_final: 0.8738 (ttp80) REVERT: J 82 ARG cc_start: 0.7328 (ttp80) cc_final: 0.6934 (ttp80) REVERT: J 110 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7495 (pt0) outliers start: 15 outliers final: 10 residues processed: 165 average time/residue: 0.3684 time to fit residues: 91.7803 Evaluate side-chains 145 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain J residue 110 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 167 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 263 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 GLN G 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.101534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.068694 restraints weight = 123688.611| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.50 r_work: 0.2764 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 22705 Z= 0.234 Angle : 0.532 5.827 31008 Z= 0.278 Chirality : 0.044 0.142 3591 Planarity : 0.004 0.038 3808 Dihedral : 4.604 32.158 3205 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.08 % Allowed : 12.05 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.16), residues: 2705 helix: 2.05 (0.20), residues: 663 sheet: -0.78 (0.18), residues: 803 loop : -0.71 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 66 TYR 0.019 0.001 TYR K 182 PHE 0.012 0.001 PHE A 142 TRP 0.017 0.001 TRP F 168 HIS 0.004 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00550 (22677) covalent geometry : angle 0.52618 (30940) SS BOND : bond 0.00411 ( 16) SS BOND : angle 1.07531 ( 32) hydrogen bonds : bond 0.04422 ( 980) hydrogen bonds : angle 5.34843 ( 2967) link_BETA1-4 : bond 0.00338 ( 4) link_BETA1-4 : angle 2.32557 ( 12) link_NAG-ASN : bond 0.00448 ( 8) link_NAG-ASN : angle 1.97014 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 PHE cc_start: 0.7434 (m-80) cc_final: 0.6884 (m-10) REVERT: B 12 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7112 (tp30) REVERT: B 371 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7425 (mt) REVERT: C 241 MET cc_start: 0.8451 (mmp) cc_final: 0.8191 (mmp) REVERT: D 169 HIS cc_start: 0.7980 (OUTLIER) cc_final: 0.7525 (p-80) REVERT: E 36 MET cc_start: 0.9227 (tmm) cc_final: 0.9023 (ttm) REVERT: J 82 ARG cc_start: 0.7352 (ttp80) cc_final: 0.7089 (ttp80) REVERT: J 110 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7623 (pt0) outliers start: 27 outliers final: 18 residues processed: 161 average time/residue: 0.3625 time to fit residues: 88.1193 Evaluate side-chains 152 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 183 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 165 optimal weight: 1.9990 chunk 236 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.070259 restraints weight = 122781.497| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.66 r_work: 0.2790 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22705 Z= 0.159 Angle : 0.495 5.147 31008 Z= 0.258 Chirality : 0.043 0.139 3591 Planarity : 0.004 0.036 3808 Dihedral : 4.363 29.367 3205 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.96 % Allowed : 12.81 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.16), residues: 2705 helix: 2.24 (0.20), residues: 651 sheet: -0.78 (0.18), residues: 802 loop : -0.68 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 66 TYR 0.010 0.001 TYR K 182 PHE 0.010 0.001 PHE A 142 TRP 0.009 0.001 TRP G 161 HIS 0.004 0.001 HIS F 194 Details of bonding type rmsd covalent geometry : bond 0.00371 (22677) covalent geometry : angle 0.49085 (30940) SS BOND : bond 0.00438 ( 16) SS BOND : angle 1.02645 ( 32) hydrogen bonds : bond 0.04107 ( 980) hydrogen bonds : angle 5.12071 ( 2967) link_BETA1-4 : bond 0.00119 ( 4) link_BETA1-4 : angle 1.72694 ( 12) link_NAG-ASN : bond 0.00159 ( 8) link_NAG-ASN : angle 1.77581 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 371 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7427 (mt) REVERT: C 241 MET cc_start: 0.8368 (mmp) cc_final: 0.8143 (mmp) REVERT: D 169 HIS cc_start: 0.7966 (OUTLIER) cc_final: 0.7517 (p-80) REVERT: E 155 ARG cc_start: 0.9007 (ttp80) cc_final: 0.8688 (ttt-90) REVERT: E 239 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8069 (mt-10) REVERT: J 82 ARG cc_start: 0.7381 (ttp80) cc_final: 0.6916 (ttp80) outliers start: 24 outliers final: 20 residues processed: 156 average time/residue: 0.3471 time to fit residues: 83.2288 Evaluate side-chains 151 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 183 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 252 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 chunk 175 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 203 optimal weight: 30.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.101356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.069609 restraints weight = 123197.467| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.63 r_work: 0.2776 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 22705 Z= 0.207 Angle : 0.514 5.640 31008 Z= 0.267 Chirality : 0.043 0.142 3591 Planarity : 0.004 0.039 3808 Dihedral : 4.386 31.138 3205 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.24 % Allowed : 12.97 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.16), residues: 2705 helix: 2.19 (0.20), residues: 651 sheet: -0.81 (0.17), residues: 805 loop : -0.71 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 66 TYR 0.011 0.001 TYR K 105 PHE 0.011 0.001 PHE A 142 TRP 0.009 0.001 TRP F 101 HIS 0.003 0.001 HIS E 297 Details of bonding type rmsd covalent geometry : bond 0.00489 (22677) covalent geometry : angle 0.50951 (30940) SS BOND : bond 0.00422 ( 16) SS BOND : angle 1.04746 ( 32) hydrogen bonds : bond 0.04127 ( 980) hydrogen bonds : angle 5.05695 ( 2967) link_BETA1-4 : bond 0.00238 ( 4) link_BETA1-4 : angle 1.90706 ( 12) link_NAG-ASN : bond 0.00375 ( 8) link_NAG-ASN : angle 1.87605 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 371 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7446 (mt) REVERT: C 49 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: C 241 MET cc_start: 0.8436 (mmp) cc_final: 0.8221 (mmp) REVERT: C 259 SER cc_start: 0.9404 (OUTLIER) cc_final: 0.9015 (p) REVERT: D 169 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7489 (p-80) REVERT: E 155 ARG cc_start: 0.9010 (ttp80) cc_final: 0.8710 (ttt-90) REVERT: J 110 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7609 (pt0) outliers start: 31 outliers final: 24 residues processed: 162 average time/residue: 0.3383 time to fit residues: 84.0305 Evaluate side-chains 155 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 183 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 109 optimal weight: 4.9990 chunk 245 optimal weight: 40.0000 chunk 44 optimal weight: 4.9990 chunk 217 optimal weight: 20.0000 chunk 216 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 256 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 371 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.101520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.068931 restraints weight = 122995.383| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.61 r_work: 0.2762 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22705 Z= 0.183 Angle : 0.502 6.175 31008 Z= 0.260 Chirality : 0.043 0.141 3591 Planarity : 0.004 0.063 3808 Dihedral : 4.359 30.393 3205 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.48 % Allowed : 12.97 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.16), residues: 2705 helix: 2.22 (0.20), residues: 651 sheet: -0.81 (0.17), residues: 802 loop : -0.71 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 82 TYR 0.010 0.001 TYR E 275 PHE 0.011 0.001 PHE A 142 TRP 0.008 0.001 TRP F 101 HIS 0.004 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00432 (22677) covalent geometry : angle 0.49799 (30940) SS BOND : bond 0.00425 ( 16) SS BOND : angle 1.02871 ( 32) hydrogen bonds : bond 0.04002 ( 980) hydrogen bonds : angle 4.96484 ( 2967) link_BETA1-4 : bond 0.00226 ( 4) link_BETA1-4 : angle 1.70111 ( 12) link_NAG-ASN : bond 0.00255 ( 8) link_NAG-ASN : angle 1.80493 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 371 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7438 (mt) REVERT: C 49 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8403 (mp0) REVERT: C 259 SER cc_start: 0.9372 (OUTLIER) cc_final: 0.8985 (p) REVERT: D 169 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7480 (p-80) REVERT: E 155 ARG cc_start: 0.9006 (ttp80) cc_final: 0.8735 (ttt-90) REVERT: J 82 ARG cc_start: 0.7396 (ttp80) cc_final: 0.6962 (ttp80) REVERT: J 110 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7612 (pt0) outliers start: 37 outliers final: 27 residues processed: 163 average time/residue: 0.3564 time to fit residues: 88.4694 Evaluate side-chains 156 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 183 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 182 optimal weight: 0.3980 chunk 208 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.101870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.069387 restraints weight = 123120.393| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.54 r_work: 0.2790 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22705 Z= 0.155 Angle : 0.489 6.660 31008 Z= 0.252 Chirality : 0.043 0.139 3591 Planarity : 0.004 0.046 3808 Dihedral : 4.285 28.485 3205 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.96 % Favored : 96.01 % Rotamer: Outliers : 1.48 % Allowed : 13.25 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.16), residues: 2705 helix: 2.31 (0.20), residues: 651 sheet: -0.79 (0.17), residues: 805 loop : -0.68 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 82 TYR 0.010 0.001 TYR E 275 PHE 0.010 0.001 PHE A 142 TRP 0.008 0.001 TRP G 161 HIS 0.004 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00365 (22677) covalent geometry : angle 0.48455 (30940) SS BOND : bond 0.00437 ( 16) SS BOND : angle 1.00918 ( 32) hydrogen bonds : bond 0.03855 ( 980) hydrogen bonds : angle 4.84924 ( 2967) link_BETA1-4 : bond 0.00239 ( 4) link_BETA1-4 : angle 1.64561 ( 12) link_NAG-ASN : bond 0.00227 ( 8) link_NAG-ASN : angle 1.75244 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 371 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7491 (mt) REVERT: C 49 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: C 241 MET cc_start: 0.8168 (mmp) cc_final: 0.7934 (mmp) REVERT: C 259 SER cc_start: 0.9353 (OUTLIER) cc_final: 0.8959 (p) REVERT: C 368 MET cc_start: 0.5905 (tmm) cc_final: 0.5661 (tmm) REVERT: D 169 HIS cc_start: 0.8001 (OUTLIER) cc_final: 0.7486 (p-80) REVERT: D 191 THR cc_start: 0.9301 (m) cc_final: 0.9057 (p) REVERT: E 155 ARG cc_start: 0.8976 (ttp80) cc_final: 0.8717 (ttt-90) REVERT: J 82 ARG cc_start: 0.7401 (ttp80) cc_final: 0.7010 (ttp80) REVERT: J 110 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7615 (pt0) outliers start: 37 outliers final: 25 residues processed: 168 average time/residue: 0.3484 time to fit residues: 89.0920 Evaluate side-chains 158 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 183 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 124 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 204 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 203 optimal weight: 30.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.102349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.069974 restraints weight = 122373.901| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.48 r_work: 0.2805 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22705 Z= 0.124 Angle : 0.480 7.531 31008 Z= 0.247 Chirality : 0.043 0.137 3591 Planarity : 0.004 0.047 3808 Dihedral : 4.204 26.436 3205 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 1.24 % Allowed : 13.45 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.16), residues: 2705 helix: 2.39 (0.20), residues: 651 sheet: -0.70 (0.18), residues: 778 loop : -0.66 (0.18), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 155 TYR 0.010 0.001 TYR E 275 PHE 0.008 0.001 PHE A 142 TRP 0.008 0.001 TRP G 161 HIS 0.004 0.001 HIS E 297 Details of bonding type rmsd covalent geometry : bond 0.00292 (22677) covalent geometry : angle 0.47612 (30940) SS BOND : bond 0.00447 ( 16) SS BOND : angle 1.00060 ( 32) hydrogen bonds : bond 0.03715 ( 980) hydrogen bonds : angle 4.74965 ( 2967) link_BETA1-4 : bond 0.00255 ( 4) link_BETA1-4 : angle 1.55354 ( 12) link_NAG-ASN : bond 0.00139 ( 8) link_NAG-ASN : angle 1.68401 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 196 TYR cc_start: 0.8899 (t80) cc_final: 0.8672 (t80) REVERT: C 259 SER cc_start: 0.9310 (OUTLIER) cc_final: 0.8898 (p) REVERT: C 368 MET cc_start: 0.5914 (tmm) cc_final: 0.5671 (tmm) REVERT: D 169 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.7530 (p-80) REVERT: D 191 THR cc_start: 0.9296 (m) cc_final: 0.9075 (p) REVERT: E 155 ARG cc_start: 0.8944 (ttp80) cc_final: 0.8654 (ttt-90) REVERT: J 82 ARG cc_start: 0.7409 (ttp80) cc_final: 0.7123 (ttp80) REVERT: J 110 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7643 (pt0) outliers start: 31 outliers final: 26 residues processed: 159 average time/residue: 0.3525 time to fit residues: 85.4637 Evaluate side-chains 160 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 8 optimal weight: 0.1980 chunk 149 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 230 optimal weight: 3.9990 chunk 248 optimal weight: 0.5980 chunk 263 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 168 optimal weight: 0.0980 chunk 68 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.103252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.071828 restraints weight = 122186.101| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.35 r_work: 0.2836 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22705 Z= 0.092 Angle : 0.466 6.895 31008 Z= 0.238 Chirality : 0.042 0.134 3591 Planarity : 0.004 0.044 3808 Dihedral : 4.055 24.680 3205 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.40 % Favored : 96.56 % Rotamer: Outliers : 0.96 % Allowed : 13.53 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.16), residues: 2705 helix: 2.56 (0.20), residues: 651 sheet: -0.64 (0.18), residues: 772 loop : -0.58 (0.18), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 155 TYR 0.009 0.001 TYR J 41 PHE 0.007 0.001 PHE D 361 TRP 0.008 0.001 TRP E 120 HIS 0.004 0.001 HIS E 297 Details of bonding type rmsd covalent geometry : bond 0.00214 (22677) covalent geometry : angle 0.46264 (30940) SS BOND : bond 0.00468 ( 16) SS BOND : angle 1.00458 ( 32) hydrogen bonds : bond 0.03528 ( 980) hydrogen bonds : angle 4.64799 ( 2967) link_BETA1-4 : bond 0.00298 ( 4) link_BETA1-4 : angle 1.45061 ( 12) link_NAG-ASN : bond 0.00043 ( 8) link_NAG-ASN : angle 1.56885 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5410 Ramachandran restraints generated. 2705 Oldfield, 0 Emsley, 2705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 259 SER cc_start: 0.9185 (OUTLIER) cc_final: 0.8809 (p) REVERT: C 368 MET cc_start: 0.6013 (tmm) cc_final: 0.5763 (tmm) REVERT: D 169 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.7456 (p-80) REVERT: D 191 THR cc_start: 0.9297 (m) cc_final: 0.9072 (p) REVERT: E 155 ARG cc_start: 0.8886 (ttp80) cc_final: 0.8632 (ttt-90) REVERT: J 82 ARG cc_start: 0.7442 (ttp80) cc_final: 0.7160 (ttp80) REVERT: J 110 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7644 (pt0) outliers start: 24 outliers final: 20 residues processed: 163 average time/residue: 0.3484 time to fit residues: 85.6961 Evaluate side-chains 158 residues out of total 2498 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 350 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain J residue 110 GLU Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 51 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 174 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 241 optimal weight: 10.0000 chunk 160 optimal weight: 0.4980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.103120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.070690 restraints weight = 122572.682| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.51 r_work: 0.2819 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22705 Z= 0.108 Angle : 0.468 7.410 31008 Z= 0.240 Chirality : 0.042 0.134 3591 Planarity : 0.004 0.043 3808 Dihedral : 4.014 24.657 3205 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 0.96 % Allowed : 13.65 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.17), residues: 2705 helix: 2.55 (0.20), residues: 651 sheet: -0.67 (0.18), residues: 802 loop : -0.52 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 155 TYR 0.018 0.001 TYR C 196 PHE 0.008 0.001 PHE D 219 TRP 0.009 0.001 TRP F 40 HIS 0.004 0.001 HIS E 297 Details of bonding type rmsd covalent geometry : bond 0.00254 (22677) covalent geometry : angle 0.46410 (30940) SS BOND : bond 0.00461 ( 16) SS BOND : angle 0.99968 ( 32) hydrogen bonds : bond 0.03528 ( 980) hydrogen bonds : angle 4.59369 ( 2967) link_BETA1-4 : bond 0.00280 ( 4) link_BETA1-4 : angle 1.52838 ( 12) link_NAG-ASN : bond 0.00128 ( 8) link_NAG-ASN : angle 1.60111 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9101.98 seconds wall clock time: 155 minutes 6.27 seconds (9306.27 seconds total)