Starting phenix.real_space_refine on Wed Aug 27 00:43:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8st2_40755/08_2025/8st2_40755_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8st2_40755/08_2025/8st2_40755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8st2_40755/08_2025/8st2_40755_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8st2_40755/08_2025/8st2_40755_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8st2_40755/08_2025/8st2_40755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8st2_40755/08_2025/8st2_40755.map" } resolution = 2.94 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 120 5.16 5 Na 1 4.78 5 C 14419 2.51 5 N 3599 2.21 5 O 4108 1.98 5 H 21937 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 44184 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 6257 Classifications: {'peptide': 379} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 359} Chain: "B" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 6257 Classifications: {'peptide': 379} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 359} Chain: "C" Number of atoms: 5995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 5995 Classifications: {'peptide': 366} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 343} Chain breaks: 1 Chain: "D" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 6257 Classifications: {'peptide': 379} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 359} Chain: "E" Number of atoms: 5995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 5995 Classifications: {'peptide': 366} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 343} 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: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" 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: 6.42, per 1000 atoms: 0.15 Number of scatterers: 44184 At special positions: 0 Unit cell: (125.12, 203.186, 145.438, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 Na 1 11.00 O 4108 8.00 N 3599 7.00 C 14419 6.00 H 21937 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=2.04 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 200 " distance=2.05 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.04 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=2.03 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 81 " " NAG A 703 " - " ASN A 148 " " NAG B 701 " - " ASN B 31 " " NAG B 702 " - " ASN B 81 " " NAG B 703 " - " ASN B 148 " " NAG D 701 " - " ASN D 31 " " NAG D 702 " - " ASN D 81 " " NAG D 703 " - " ASN D 148 " " NAG H 1 " - " ASN C 143 " " NAG I 1 " - " ASN E 143 " Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5248 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 39 sheets defined 31.4% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 6 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 224 Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.747A pdb=" N LEU A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 5.032A pdb=" N VAL A 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.529A pdb=" N GLY A 246 " --> pdb=" O SER A 243 " (cutoff:3.500A) 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: 5.587A 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 removed outlier: 3.575A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Proline residue: A 379 - end of helix Processing helix chain 'B' and resid 6 through 19 removed outlier: 4.017A pdb=" N GLU B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 removed outlier: 4.172A pdb=" N GLU B 80 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 224 through 234 removed outlier: 3.722A pdb=" N LEU B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 removed outlier: 4.314A 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 322 Processing helix chain 'B' and resid 324 through 330 removed outlier: 3.835A pdb=" N ARG B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 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: 3.725A 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: 3.932A 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: 4.364A pdb=" N ILE C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Proline residue: C 219 - end of helix removed outlier: 3.685A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.911A pdb=" N VAL C 230 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 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: 5.853A 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 6 through 19 Processing helix chain 'D' and resid 75 through 79 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: 4.573A pdb=" N ILE D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.781A pdb=" N LEU D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 241 removed outlier: 4.312A pdb=" N VAL D 238 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 246 removed outlier: 3.548A pdb=" N GLY D 246 " --> pdb=" O SER D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 267 Processing helix chain 'D' and resid 278 through 306 Processing helix chain 'D' and resid 315 through 330 removed outlier: 5.505A 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: 3.661A 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: 4.180A 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 225 Processing helix chain 'E' and resid 226 through 233 removed outlier: 4.589A pdb=" N VAL E 230 " --> pdb=" O ALA E 227 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 233 " --> pdb=" O VAL E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 removed outlier: 3.596A pdb=" N GLY E 238 " --> pdb=" O SER E 235 " (cutoff:3.500A) 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: 3.875A pdb=" N ALA E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 364 Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.880A pdb=" N LEU E 370 " --> pdb=" O ILE E 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 88 Processing helix chain 'F' and resid 126 through 133 Processing helix chain 'F' and resid 187 through 192 Processing helix chain 'G' and resid 29 through 33 removed outlier: 3.513A pdb=" N TYR G 33 " --> pdb=" O PHE G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 66 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 removed outlier: 3.805A pdb=" N GLU J 192 " --> pdb=" O LYS J 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 33 removed outlier: 3.733A pdb=" N TYR K 33 " --> pdb=" O PHE K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 66 Processing helix chain 'K' and resid 163 through 165 No H-bonds generated for 'chain 'K' and resid 163 through 165' Processing helix chain 'K' and resid 207 through 210 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 88 removed outlier: 4.075A pdb=" N ARG A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 88 removed outlier: 4.075A pdb=" N ARG A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N MET A 56 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP A 49 " --> pdb=" O MET A 56 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR A 58 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N HIS A 68 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.574A 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: 4.333A pdb=" N SER A 155 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 189 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG A 214 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.479A 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: 3.914A pdb=" N ARG B 122 " --> pdb=" O PHE B 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.914A pdb=" N ARG B 122 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N MET B 56 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASP B 49 " --> pdb=" O MET B 56 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B 58 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N HIS B 68 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.402A 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: 4.340A pdb=" N SER B 155 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 189 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG B 214 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 5.372A 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: 4.114A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.550A 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: 4.114A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP C 62 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE C 51 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER C 44 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN C 55 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU C 63 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR C 32 " --> pdb=" O GLU C 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.190A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.802A 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: 5.190A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 84 through 88 removed outlier: 3.866A pdb=" N ARG D 122 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY D 121 " --> pdb=" O ASP D 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 84 through 88 removed outlier: 3.866A pdb=" N ARG D 122 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY D 121 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N MET D 56 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP D 49 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR D 58 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N HIS D 68 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU D 37 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.454A pdb=" N SER D 155 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG D 195 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 189 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG D 214 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE D 185 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 79 through 83 removed outlier: 4.147A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 79 through 83 removed outlier: 4.147A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE E 51 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL E 45 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR E 53 " --> pdb=" O ILE E 43 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP E 57 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU E 39 " --> pdb=" O TRP E 57 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR E 59 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL E 37 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLU E 61 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU E 35 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N GLU E 63 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N VAL E 33 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL E 31 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL E 161 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL E 33 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.157A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE E 204 " --> pdb=" O VAL E 181 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.157A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.570A pdb=" N GLU F 110 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY F 89 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU F 38 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR F 54 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP F 40 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 119 through 123 Processing sheet with id=AC3, first strand: chain 'F' and resid 119 through 123 removed outlier: 6.132A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER F 179 " --> pdb=" O THR F 169 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 158 through 160 removed outlier: 3.951A pdb=" N TRP F 153 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS F 152 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR F 198 " --> pdb=" O LYS F 154 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.435A pdb=" N ILE G 35 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU G 51 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TRP G 37 " --> pdb=" O ILE G 49 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 129 through 131 removed outlier: 4.365A pdb=" N GLY G 146 " --> pdb=" O LEU G 131 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER G 186 " --> pdb=" O CYS G 147 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR G 182 " --> pdb=" O GLY G 151 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 129 through 131 removed outlier: 4.365A pdb=" N GLY G 146 " --> pdb=" O LEU G 131 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER G 186 " --> pdb=" O CYS G 147 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR G 182 " --> pdb=" O GLY G 151 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N SER G 185 " --> pdb=" O PRO G 174 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N SER G 187 " --> pdb=" O THR G 172 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR G 172 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR G 189 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL G 170 " --> pdb=" O THR G 189 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 201 through 206 removed outlier: 4.022A pdb=" N CYS G 202 " --> pdb=" O LYS G 215 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS G 215 " --> pdb=" O CYS G 202 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G 204 " --> pdb=" O VAL G 213 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.106A pdb=" N GLY J 89 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP J 40 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 119 through 123 removed outlier: 3.587A pdb=" N ASN J 142 " --> pdb=" O THR J 119 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL J 138 " --> pdb=" O PHE J 123 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER J 179 " --> pdb=" O THR J 169 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 149 through 152 Processing sheet with id=AD5, first strand: chain 'J' and resid 154 through 155 Processing sheet with id=AD6, first strand: chain 'J' and resid 196 through 198 Processing sheet with id=AD7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.453A pdb=" N ILE K 35 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU K 51 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TRP K 37 " --> pdb=" O ILE K 49 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 127 through 131 removed outlier: 3.537A pdb=" N LEU K 148 " --> pdb=" O TYR K 129 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR K 182 " --> pdb=" O GLY K 151 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 127 through 131 removed outlier: 3.537A pdb=" N LEU K 148 " --> pdb=" O TYR K 129 " (cutoff:3.500A) removed outlier: 6.290A 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 removed outlier: 4.022A pdb=" N VAL K 143 " --> pdb=" O VAL K 190 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL K 190 " --> pdb=" O VAL K 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'K' and resid 158 through 161 removed outlier: 4.412A pdb=" N CYS K 202 " --> pdb=" O LYS K 215 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS K 215 " --> pdb=" O CYS K 202 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 2982 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: 10.40 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 21912 1.04 - 1.24: 2939 1.24 - 1.45: 7032 1.45 - 1.65: 12708 1.65 - 1.85: 183 Bond restraints: 44774 Sorted by residual: bond pdb=" C VAL A 189 " pdb=" N GLY A 190 " ideal model delta sigma weight residual 1.332 1.344 -0.012 6.60e-03 2.30e+04 3.07e+00 bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N ASP J 1 " pdb=" CA ASP J 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.72e+00 bond pdb=" N ASP J 1 " pdb=" H ASP J 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" N ASP F 1 " pdb=" H ASP F 1 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.17e+00 ... (remaining 44769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 79925 1.63 - 3.25: 857 3.25 - 4.88: 139 4.88 - 6.51: 10 6.51 - 8.14: 4 Bond angle restraints: 80935 Sorted by residual: angle pdb=" CB ARG F 24 " pdb=" CG ARG F 24 " pdb=" CD ARG F 24 " ideal model delta sigma weight residual 111.30 119.04 -7.74 2.30e+00 1.89e-01 1.13e+01 angle pdb=" N PRO B 380 " pdb=" CD PRO B 380 " pdb=" CG PRO B 380 " ideal model delta sigma weight residual 103.20 98.49 4.71 1.50e+00 4.44e-01 9.86e+00 angle pdb=" N ASP G 180 " pdb=" CA ASP G 180 " pdb=" C ASP G 180 " ideal model delta sigma weight residual 114.39 110.24 4.15 1.45e+00 4.76e-01 8.20e+00 angle pdb=" CB MET E 241 " pdb=" CG MET E 241 " pdb=" SD MET E 241 " ideal model delta sigma weight residual 112.70 120.84 -8.14 3.00e+00 1.11e-01 7.36e+00 angle pdb=" CA PRO B 380 " pdb=" N PRO B 380 " pdb=" CD PRO B 380 " ideal model delta sigma weight residual 112.00 108.39 3.61 1.40e+00 5.10e-01 6.64e+00 ... (remaining 80930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.70: 19958 21.70 - 43.41: 1220 43.41 - 65.11: 245 65.11 - 86.81: 45 86.81 - 108.52: 10 Dihedral angle restraints: 21478 sinusoidal: 11626 harmonic: 9852 Sorted by residual: dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 93 " pdb=" CB CYS F 93 " ideal model delta sinusoidal sigma weight residual 93.00 160.46 -67.46 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CB CYS C 130 " pdb=" SG CYS C 130 " pdb=" SG CYS C 144 " pdb=" CB CYS C 144 " ideal model delta sinusoidal sigma weight residual 93.00 38.10 54.90 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 38.30 54.70 1 1.00e+01 1.00e-02 4.05e+01 ... (remaining 21475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2929 0.052 - 0.105: 576 0.105 - 0.157: 115 0.157 - 0.210: 1 0.210 - 0.262: 2 Chirality restraints: 3623 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 0.26 2.00e-01 2.50e+01 1.72e+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 -2.53 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 3620 not shown) Planarity restraints: 6421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 379 " -0.047 5.00e-02 4.00e+02 7.00e-02 7.83e+00 pdb=" N PRO B 380 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 380 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 380 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 379 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO A 380 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 380 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 380 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 218 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C LEU A 218 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU A 218 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE A 219 " -0.010 2.00e-02 2.50e+03 ... (remaining 6418 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.79: 73 1.79 - 2.49: 31751 2.49 - 3.20: 133130 3.20 - 3.90: 180430 3.90 - 4.60: 284785 Nonbonded interactions: 630169 Sorted by model distance: nonbonded pdb=" O PRO B 242 " pdb=" HG CYS B 245 " model vdw 1.088 2.620 nonbonded pdb=" O PRO C 234 " pdb=" HG CYS C 237 " model vdw 1.249 2.620 nonbonded pdb=" OE1 GLU F 86 " pdb=" H GLU F 86 " model vdw 1.441 2.450 nonbonded pdb=" OD1 ASN F 142 " pdb="HD22 ASN F 143 " model vdw 1.442 2.450 nonbonded pdb=" OE1 GLU G 90 " pdb=" H GLU G 90 " model vdw 1.523 2.450 ... (remaining 630164 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' selection = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = (chain 'E' and resid 1 through 372) } 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.320 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 36.760 Find NCS groups from input model: 0.550 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:9.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 0.057 22868 Z= 0.205 Angle : 0.552 8.137 31233 Z= 0.277 Chirality : 0.044 0.262 3623 Planarity : 0.004 0.070 3833 Dihedral : 15.403 108.517 8443 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % 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 (0.17), residues: 2719 helix: 1.43 (0.21), residues: 674 sheet: -0.24 (0.18), residues: 762 loop : -0.36 (0.18), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 24 TYR 0.021 0.001 TYR K 103 PHE 0.017 0.001 PHE A 290 TRP 0.019 0.001 TRP B 317 HIS 0.006 0.001 HIS E 46 Details of bonding type rmsd covalent geometry : bond 0.00483 (22837) covalent geometry : angle 0.54597 (31156) SS BOND : bond 0.00622 ( 16) SS BOND : angle 1.31820 ( 32) hydrogen bonds : bond 0.19685 ( 988) hydrogen bonds : angle 8.24204 ( 2982) link_BETA1-4 : bond 0.00248 ( 4) link_BETA1-4 : angle 2.26532 ( 12) link_NAG-ASN : bond 0.00230 ( 11) link_NAG-ASN : angle 1.82979 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.995 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: F 24 ARG cc_start: 0.7472 (mtp-110) cc_final: 0.7159 (ttp80) REVERT: F 195 ASN cc_start: 0.8582 (m-40) cc_final: 0.8335 (m-40) REVERT: J 9 LEU cc_start: 0.8784 (mm) cc_final: 0.8325 (tp) REVERT: J 24 ARG cc_start: 0.7367 (mtp-110) cc_final: 0.6947 (ttp-110) REVERT: J 66 ARG cc_start: 0.7484 (ptp-170) cc_final: 0.6927 (ptp-170) REVERT: J 215 ASN cc_start: 0.6637 (t0) cc_final: 0.6409 (t0) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 1.4805 time to fit residues: 389.6369 Evaluate side-chains 190 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 43 GLN K 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.088612 restraints weight = 91539.335| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.66 r_work: 0.2790 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 22868 Z= 0.282 Angle : 0.610 6.045 31233 Z= 0.322 Chirality : 0.047 0.183 3623 Planarity : 0.005 0.046 3833 Dihedral : 6.846 72.330 3285 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.45 % Favored : 95.51 % Rotamer: Outliers : 1.24 % Allowed : 13.43 % Favored : 85.33 % 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: -0.04 (0.16), residues: 2719 helix: 1.56 (0.20), residues: 682 sheet: -0.30 (0.18), residues: 785 loop : -0.66 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 7 TYR 0.015 0.002 TYR C 275 PHE 0.019 0.002 PHE A 290 TRP 0.012 0.001 TRP D 62 HIS 0.006 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00666 (22837) covalent geometry : angle 0.60186 (31156) SS BOND : bond 0.00835 ( 16) SS BOND : angle 1.92919 ( 32) hydrogen bonds : bond 0.05744 ( 988) hydrogen bonds : angle 5.86866 ( 2982) link_BETA1-4 : bond 0.00215 ( 4) link_BETA1-4 : angle 2.96424 ( 12) link_NAG-ASN : bond 0.00459 ( 11) link_NAG-ASN : angle 1.95977 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 1.252 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: A 333 LYS cc_start: 0.8098 (ptpt) cc_final: 0.7864 (pmtt) REVERT: C 36 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8349 (tmm) REVERT: E 154 ASP cc_start: 0.8745 (p0) cc_final: 0.8453 (p0) REVERT: F 24 ARG cc_start: 0.7695 (mtp-110) cc_final: 0.7344 (ttp80) REVERT: F 84 GLU cc_start: 0.7653 (mp0) cc_final: 0.7416 (mp0) REVERT: F 129 GLN cc_start: 0.7967 (tp-100) cc_final: 0.7691 (tp-100) REVERT: F 142 ASN cc_start: 0.6860 (t0) cc_final: 0.6608 (m-40) REVERT: F 166 ASN cc_start: 0.7995 (m-40) cc_final: 0.7620 (m-40) REVERT: J 9 LEU cc_start: 0.8788 (mm) cc_final: 0.8446 (tt) REVERT: J 24 ARG cc_start: 0.7555 (mtp-110) cc_final: 0.6959 (ttm110) REVERT: J 215 ASN cc_start: 0.7268 (t0) cc_final: 0.6814 (t0) outliers start: 31 outliers final: 15 residues processed: 229 average time/residue: 1.3853 time to fit residues: 368.3214 Evaluate side-chains 214 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 155 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 168 optimal weight: 0.2980 chunk 142 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 202 optimal weight: 40.0000 chunk 110 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 221 optimal weight: 20.0000 chunk 166 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 171 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.129650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.089808 restraints weight = 90967.461| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.41 r_work: 0.2829 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22868 Z= 0.141 Angle : 0.526 5.764 31233 Z= 0.274 Chirality : 0.044 0.159 3623 Planarity : 0.004 0.061 3833 Dihedral : 5.643 50.454 3285 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.04 % Allowed : 14.27 % Favored : 84.70 % 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: 2719 helix: 1.69 (0.20), residues: 688 sheet: -0.30 (0.18), residues: 765 loop : -0.65 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 7 TYR 0.016 0.001 TYR G 105 PHE 0.019 0.001 PHE F 144 TRP 0.012 0.001 TRP B 317 HIS 0.003 0.001 HIS G 171 Details of bonding type rmsd covalent geometry : bond 0.00320 (22837) covalent geometry : angle 0.51983 (31156) SS BOND : bond 0.00646 ( 16) SS BOND : angle 1.42769 ( 32) hydrogen bonds : bond 0.04913 ( 988) hydrogen bonds : angle 5.39108 ( 2982) link_BETA1-4 : bond 0.00488 ( 4) link_BETA1-4 : angle 2.39960 ( 12) link_NAG-ASN : bond 0.00182 ( 11) link_NAG-ASN : angle 1.76209 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 1.173 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: A 333 LYS cc_start: 0.8107 (ptpt) cc_final: 0.7847 (pmtt) REVERT: E 154 ASP cc_start: 0.8695 (p0) cc_final: 0.8438 (p0) REVERT: F 110 GLU cc_start: 0.7538 (pm20) cc_final: 0.7204 (pm20) REVERT: F 195 ASN cc_start: 0.9009 (m-40) cc_final: 0.8687 (m-40) REVERT: J 9 LEU cc_start: 0.8859 (mm) cc_final: 0.8507 (tt) REVERT: J 24 ARG cc_start: 0.7437 (mtp-110) cc_final: 0.6823 (ttm110) REVERT: J 128 GLU cc_start: 0.9269 (mp0) cc_final: 0.8965 (mp0) REVERT: J 190 GLU cc_start: 0.6992 (tp30) cc_final: 0.6080 (tp30) REVERT: J 195 ASN cc_start: 0.9258 (p0) cc_final: 0.9033 (p0) REVERT: J 215 ASN cc_start: 0.7236 (t0) cc_final: 0.6775 (t0) outliers start: 26 outliers final: 14 residues processed: 215 average time/residue: 1.3033 time to fit residues: 326.3902 Evaluate side-chains 202 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 128 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 251 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 218 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.129850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.081668 restraints weight = 90634.164| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.91 r_work: 0.2838 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22868 Z= 0.154 Angle : 0.518 6.262 31233 Z= 0.268 Chirality : 0.044 0.155 3623 Planarity : 0.004 0.045 3833 Dihedral : 4.941 37.662 3285 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.12 % Favored : 95.84 % Rotamer: Outliers : 1.24 % Allowed : 14.39 % Favored : 84.38 % 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: 2719 helix: 1.78 (0.20), residues: 691 sheet: -0.33 (0.17), residues: 785 loop : -0.64 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 24 TYR 0.015 0.001 TYR C 275 PHE 0.019 0.001 PHE F 214 TRP 0.012 0.001 TRP B 317 HIS 0.009 0.001 HIS J 194 Details of bonding type rmsd covalent geometry : bond 0.00361 (22837) covalent geometry : angle 0.51085 (31156) SS BOND : bond 0.00665 ( 16) SS BOND : angle 1.49669 ( 32) hydrogen bonds : bond 0.04482 ( 988) hydrogen bonds : angle 5.12016 ( 2982) link_BETA1-4 : bond 0.00325 ( 4) link_BETA1-4 : angle 2.46023 ( 12) link_NAG-ASN : bond 0.00239 ( 11) link_NAG-ASN : angle 1.77761 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 1.309 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: A 333 LYS cc_start: 0.8097 (ptpt) cc_final: 0.7787 (pmtt) REVERT: C 36 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8233 (tmm) REVERT: C 101 MET cc_start: 0.8654 (tpt) cc_final: 0.8384 (tpt) REVERT: D 283 TYR cc_start: 0.8709 (t80) cc_final: 0.8457 (t80) REVERT: E 154 ASP cc_start: 0.8688 (p0) cc_final: 0.8377 (p0) REVERT: F 110 GLU cc_start: 0.7489 (pm20) cc_final: 0.7139 (pm20) REVERT: F 113 ARG cc_start: 0.7241 (ptm-80) cc_final: 0.7021 (ptt90) REVERT: F 180 MET cc_start: 0.7068 (tpp) cc_final: 0.6814 (tpp) REVERT: F 195 ASN cc_start: 0.9089 (m-40) cc_final: 0.8836 (m-40) REVERT: J 9 LEU cc_start: 0.8861 (mm) cc_final: 0.8460 (tt) REVERT: J 24 ARG cc_start: 0.7373 (mtp-110) cc_final: 0.6685 (ttm110) REVERT: J 215 ASN cc_start: 0.7423 (t0) cc_final: 0.7004 (t0) outliers start: 31 outliers final: 21 residues processed: 218 average time/residue: 1.3413 time to fit residues: 342.0654 Evaluate side-chains 209 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain K residue 150 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 52 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 249 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 217 optimal weight: 50.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 ASN ** G 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.080545 restraints weight = 90912.676| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.92 r_work: 0.2822 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 22868 Z= 0.206 Angle : 0.540 6.023 31233 Z= 0.280 Chirality : 0.044 0.153 3623 Planarity : 0.004 0.041 3833 Dihedral : 4.847 39.420 3285 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.47 % Allowed : 14.19 % Favored : 84.34 % 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: 0.00 (0.16), residues: 2719 helix: 1.75 (0.20), residues: 691 sheet: -0.37 (0.18), residues: 779 loop : -0.69 (0.18), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 7 TYR 0.019 0.001 TYR G 105 PHE 0.019 0.001 PHE F 214 TRP 0.011 0.001 TRP B 317 HIS 0.005 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00490 (22837) covalent geometry : angle 0.53292 (31156) SS BOND : bond 0.00707 ( 16) SS BOND : angle 1.44388 ( 32) hydrogen bonds : bond 0.04562 ( 988) hydrogen bonds : angle 5.03410 ( 2982) link_BETA1-4 : bond 0.00240 ( 4) link_BETA1-4 : angle 2.51990 ( 12) link_NAG-ASN : bond 0.00312 ( 11) link_NAG-ASN : angle 1.84048 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 1.078 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: A 333 LYS cc_start: 0.8097 (ptpt) cc_final: 0.7758 (pmtt) REVERT: C 36 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8308 (tmm) REVERT: E 154 ASP cc_start: 0.8679 (p0) cc_final: 0.8378 (p0) REVERT: F 18 GLN cc_start: 0.7648 (tm-30) cc_final: 0.7342 (tm-30) REVERT: F 110 GLU cc_start: 0.7524 (pm20) cc_final: 0.7179 (pm20) REVERT: F 113 ARG cc_start: 0.7356 (ptm-80) cc_final: 0.7094 (ptt90) REVERT: F 195 ASN cc_start: 0.9031 (m-40) cc_final: 0.8731 (m-40) REVERT: J 9 LEU cc_start: 0.8864 (mm) cc_final: 0.8467 (tt) REVERT: J 24 ARG cc_start: 0.7345 (mtp-110) cc_final: 0.6705 (ttm110) REVERT: J 128 GLU cc_start: 0.9283 (mp0) cc_final: 0.8883 (mp0) REVERT: J 215 ASN cc_start: 0.7583 (t0) cc_final: 0.7301 (t0) REVERT: J 218 GLU cc_start: 0.2706 (OUTLIER) cc_final: 0.1059 (mp0) outliers start: 37 outliers final: 23 residues processed: 217 average time/residue: 1.2030 time to fit residues: 304.9346 Evaluate side-chains 211 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 218 GLU Chi-restraints excluded: chain K residue 150 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 95 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 208 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 225 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 129 GLN ** G 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.130051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.081959 restraints weight = 90660.328| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.92 r_work: 0.2843 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22868 Z= 0.129 Angle : 0.500 7.349 31233 Z= 0.257 Chirality : 0.043 0.153 3623 Planarity : 0.004 0.043 3833 Dihedral : 4.542 29.314 3285 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.03 % Rotamer: Outliers : 1.36 % Allowed : 15.03 % Favored : 83.62 % 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: 2719 helix: 1.95 (0.20), residues: 689 sheet: -0.32 (0.18), residues: 779 loop : -0.63 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 216 TYR 0.015 0.001 TYR C 275 PHE 0.015 0.001 PHE F 214 TRP 0.010 0.001 TRP B 317 HIS 0.003 0.001 HIS G 171 Details of bonding type rmsd covalent geometry : bond 0.00302 (22837) covalent geometry : angle 0.49465 (31156) SS BOND : bond 0.00607 ( 16) SS BOND : angle 1.20086 ( 32) hydrogen bonds : bond 0.04133 ( 988) hydrogen bonds : angle 4.83092 ( 2982) link_BETA1-4 : bond 0.00308 ( 4) link_BETA1-4 : angle 1.94995 ( 12) link_NAG-ASN : bond 0.00167 ( 11) link_NAG-ASN : angle 1.72627 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.892 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: A 333 LYS cc_start: 0.8094 (ptpt) cc_final: 0.7756 (pmtt) REVERT: C 36 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8263 (tmm) REVERT: D 370 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7680 (mp) REVERT: E 154 ASP cc_start: 0.8648 (p0) cc_final: 0.8378 (p0) REVERT: F 18 GLN cc_start: 0.7621 (tm-30) cc_final: 0.7311 (tm-30) REVERT: F 84 GLU cc_start: 0.7807 (mp0) cc_final: 0.7514 (mp0) REVERT: F 110 GLU cc_start: 0.7539 (pm20) cc_final: 0.7197 (pm20) REVERT: F 113 ARG cc_start: 0.7310 (ptm-80) cc_final: 0.7020 (ptt90) REVERT: F 195 ASN cc_start: 0.9016 (m-40) cc_final: 0.8734 (m-40) REVERT: J 9 LEU cc_start: 0.8834 (mm) cc_final: 0.8472 (tt) REVERT: J 24 ARG cc_start: 0.7337 (mtp-110) cc_final: 0.6710 (ttm110) REVERT: J 128 GLU cc_start: 0.9250 (mp0) cc_final: 0.8893 (mp0) REVERT: J 215 ASN cc_start: 0.7550 (t0) cc_final: 0.7190 (t0) REVERT: J 218 GLU cc_start: 0.2803 (OUTLIER) cc_final: 0.1120 (mp0) outliers start: 34 outliers final: 23 residues processed: 217 average time/residue: 1.1039 time to fit residues: 281.6876 Evaluate side-chains 210 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 139 CYS Chi-restraints excluded: chain J residue 218 GLU Chi-restraints excluded: chain K residue 150 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 146 optimal weight: 3.9990 chunk 100 optimal weight: 0.0870 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 173 optimal weight: 0.0470 chunk 123 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.083265 restraints weight = 90224.234| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.92 r_work: 0.2869 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22868 Z= 0.098 Angle : 0.480 6.574 31233 Z= 0.246 Chirality : 0.042 0.148 3623 Planarity : 0.004 0.042 3833 Dihedral : 4.268 24.281 3285 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.08 % Allowed : 15.30 % Favored : 83.62 % 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: 0.19 (0.16), residues: 2719 helix: 1.97 (0.20), residues: 707 sheet: -0.27 (0.18), residues: 759 loop : -0.63 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 216 TYR 0.017 0.001 TYR G 152 PHE 0.018 0.001 PHE F 214 TRP 0.010 0.001 TRP B 317 HIS 0.003 0.000 HIS E 297 Details of bonding type rmsd covalent geometry : bond 0.00225 (22837) covalent geometry : angle 0.47485 (31156) SS BOND : bond 0.00569 ( 16) SS BOND : angle 1.11997 ( 32) hydrogen bonds : bond 0.03808 ( 988) hydrogen bonds : angle 4.63742 ( 2982) link_BETA1-4 : bond 0.00328 ( 4) link_BETA1-4 : angle 1.69972 ( 12) link_NAG-ASN : bond 0.00145 ( 11) link_NAG-ASN : angle 1.61117 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 1.217 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: A 333 LYS cc_start: 0.8130 (ptpt) cc_final: 0.7778 (pmtt) REVERT: A 358 ASP cc_start: 0.8224 (t70) cc_final: 0.7842 (t0) REVERT: C 36 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8200 (tmm) REVERT: C 70 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8446 (mtpp) REVERT: F 18 GLN cc_start: 0.7637 (tm-30) cc_final: 0.7303 (tm-30) REVERT: F 110 GLU cc_start: 0.7529 (pm20) cc_final: 0.7184 (pm20) REVERT: F 113 ARG cc_start: 0.7283 (ptm-80) cc_final: 0.6982 (ptt90) REVERT: F 195 ASN cc_start: 0.9008 (m-40) cc_final: 0.8698 (m-40) REVERT: J 9 LEU cc_start: 0.8828 (mm) cc_final: 0.8467 (tt) REVERT: J 128 GLU cc_start: 0.9250 (mp0) cc_final: 0.8914 (mp0) REVERT: J 215 ASN cc_start: 0.7548 (t0) cc_final: 0.7173 (t0) REVERT: J 218 GLU cc_start: 0.2550 (OUTLIER) cc_final: 0.0797 (mp0) outliers start: 27 outliers final: 17 residues processed: 217 average time/residue: 1.2360 time to fit residues: 316.4289 Evaluate side-chains 206 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 218 GLU Chi-restraints excluded: chain K residue 150 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 245 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 228 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 226 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 239 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.130247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.082061 restraints weight = 90906.113| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.92 r_work: 0.2845 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22868 Z= 0.149 Angle : 0.500 8.296 31233 Z= 0.256 Chirality : 0.043 0.153 3623 Planarity : 0.004 0.042 3833 Dihedral : 4.334 24.065 3285 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.20 % Allowed : 15.34 % Favored : 83.46 % 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: 0.18 (0.16), residues: 2719 helix: 1.95 (0.20), residues: 707 sheet: -0.28 (0.18), residues: 779 loop : -0.62 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 310 TYR 0.018 0.001 TYR G 152 PHE 0.014 0.001 PHE A 290 TRP 0.010 0.001 TRP B 317 HIS 0.004 0.001 HIS E 297 Details of bonding type rmsd covalent geometry : bond 0.00354 (22837) covalent geometry : angle 0.49462 (31156) SS BOND : bond 0.00641 ( 16) SS BOND : angle 1.26159 ( 32) hydrogen bonds : bond 0.03990 ( 988) hydrogen bonds : angle 4.63580 ( 2982) link_BETA1-4 : bond 0.00271 ( 4) link_BETA1-4 : angle 2.03046 ( 12) link_NAG-ASN : bond 0.00238 ( 11) link_NAG-ASN : angle 1.67334 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 1.252 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: A 333 LYS cc_start: 0.8130 (ptpt) cc_final: 0.7842 (pmtt) REVERT: A 358 ASP cc_start: 0.8254 (t70) cc_final: 0.7867 (t0) REVERT: C 36 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8263 (tmm) REVERT: C 70 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8453 (mtpp) REVERT: D 370 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7677 (mp) REVERT: F 18 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7454 (tm-30) REVERT: F 110 GLU cc_start: 0.7508 (pm20) cc_final: 0.7167 (pm20) REVERT: F 195 ASN cc_start: 0.9089 (m-40) cc_final: 0.8779 (m-40) REVERT: F 218 GLU cc_start: 0.2888 (OUTLIER) cc_final: 0.2354 (mp0) REVERT: J 9 LEU cc_start: 0.8830 (mm) cc_final: 0.8470 (tt) REVERT: J 155 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7799 (pp) REVERT: J 215 ASN cc_start: 0.7670 (t0) cc_final: 0.7268 (t0) REVERT: J 218 GLU cc_start: 0.2726 (OUTLIER) cc_final: 0.2036 (mm-30) outliers start: 30 outliers final: 19 residues processed: 210 average time/residue: 1.1647 time to fit residues: 287.7226 Evaluate side-chains 210 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 31 HIS Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 155 ILE Chi-restraints excluded: chain J residue 218 GLU Chi-restraints excluded: chain K residue 150 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 240 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 223 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 chunk 256 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 197 optimal weight: 9.9990 chunk 49 optimal weight: 0.5980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.129688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.090535 restraints weight = 90519.784| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.69 r_work: 0.2835 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22868 Z= 0.155 Angle : 0.510 9.073 31233 Z= 0.261 Chirality : 0.043 0.166 3623 Planarity : 0.004 0.104 3833 Dihedral : 4.382 23.994 3285 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.39 % Allowed : 15.46 % Favored : 83.14 % 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: 0.18 (0.16), residues: 2719 helix: 1.93 (0.20), residues: 707 sheet: -0.26 (0.18), residues: 759 loop : -0.64 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 328 TYR 0.022 0.001 TYR K 152 PHE 0.013 0.001 PHE A 290 TRP 0.010 0.001 TRP B 317 HIS 0.004 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00367 (22837) covalent geometry : angle 0.50463 (31156) SS BOND : bond 0.00635 ( 16) SS BOND : angle 1.28259 ( 32) hydrogen bonds : bond 0.04022 ( 988) hydrogen bonds : angle 4.62359 ( 2982) link_BETA1-4 : bond 0.00288 ( 4) link_BETA1-4 : angle 2.03401 ( 12) link_NAG-ASN : bond 0.00225 ( 11) link_NAG-ASN : angle 1.66665 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 1.033 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: A 333 LYS cc_start: 0.8127 (ptpt) cc_final: 0.7882 (pmtt) REVERT: A 358 ASP cc_start: 0.8229 (t70) cc_final: 0.7893 (t0) REVERT: C 36 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8264 (tmm) REVERT: C 70 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8472 (mtpp) REVERT: F 110 GLU cc_start: 0.7570 (pm20) cc_final: 0.7270 (pm20) REVERT: F 195 ASN cc_start: 0.9007 (m-40) cc_final: 0.8692 (m-40) REVERT: F 218 GLU cc_start: 0.2772 (OUTLIER) cc_final: 0.2291 (mp0) REVERT: J 9 LEU cc_start: 0.8853 (mm) cc_final: 0.8514 (tt) REVERT: J 128 GLU cc_start: 0.9224 (mp0) cc_final: 0.8744 (mp0) REVERT: J 155 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7769 (pp) REVERT: J 215 ASN cc_start: 0.7584 (t0) cc_final: 0.7196 (t0) REVERT: J 218 GLU cc_start: 0.2677 (OUTLIER) cc_final: 0.2032 (mm-30) REVERT: K 142 MET cc_start: 0.6913 (tpp) cc_final: 0.6656 (mmm) outliers start: 35 outliers final: 23 residues processed: 212 average time/residue: 1.0365 time to fit residues: 258.0438 Evaluate side-chains 210 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 31 HIS Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 155 ILE Chi-restraints excluded: chain J residue 218 GLU Chi-restraints excluded: chain K residue 150 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 191 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.089908 restraints weight = 90509.850| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.67 r_work: 0.2823 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22868 Z= 0.177 Angle : 0.526 9.638 31233 Z= 0.269 Chirality : 0.044 0.155 3623 Planarity : 0.004 0.082 3833 Dihedral : 4.468 25.483 3285 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.24 % Allowed : 15.58 % Favored : 83.18 % 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: 0.15 (0.16), residues: 2719 helix: 1.89 (0.20), residues: 707 sheet: -0.25 (0.18), residues: 759 loop : -0.66 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 328 TYR 0.025 0.001 TYR K 152 PHE 0.015 0.001 PHE A 290 TRP 0.011 0.001 TRP B 317 HIS 0.004 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00423 (22837) covalent geometry : angle 0.52069 (31156) SS BOND : bond 0.00664 ( 16) SS BOND : angle 1.32782 ( 32) hydrogen bonds : bond 0.04112 ( 988) hydrogen bonds : angle 4.63467 ( 2982) link_BETA1-4 : bond 0.00258 ( 4) link_BETA1-4 : angle 2.16232 ( 12) link_NAG-ASN : bond 0.00268 ( 11) link_NAG-ASN : angle 1.71769 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5438 Ramachandran restraints generated. 2719 Oldfield, 0 Emsley, 2719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.758 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: A 358 ASP cc_start: 0.8265 (t70) cc_final: 0.7945 (t0) REVERT: B 171 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7846 (mtp-110) REVERT: C 36 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8275 (tmm) REVERT: C 70 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8484 (mtpp) REVERT: F 110 GLU cc_start: 0.7551 (pm20) cc_final: 0.7268 (pm20) REVERT: F 129 GLN cc_start: 0.8271 (tp40) cc_final: 0.7848 (tp-100) REVERT: F 195 ASN cc_start: 0.9013 (m-40) cc_final: 0.8707 (m-40) REVERT: F 218 GLU cc_start: 0.2781 (OUTLIER) cc_final: 0.2232 (mp0) REVERT: J 9 LEU cc_start: 0.8870 (mm) cc_final: 0.8541 (tt) REVERT: J 128 GLU cc_start: 0.9206 (mp0) cc_final: 0.8741 (mp0) REVERT: J 155 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7214 (pp) REVERT: J 158 SER cc_start: 0.7512 (OUTLIER) cc_final: 0.7230 (p) REVERT: J 215 ASN cc_start: 0.7566 (t0) cc_final: 0.7207 (t0) REVERT: J 218 GLU cc_start: 0.2585 (OUTLIER) cc_final: 0.2099 (mm-30) REVERT: K 142 MET cc_start: 0.6909 (tpp) cc_final: 0.6652 (mmm) outliers start: 31 outliers final: 23 residues processed: 209 average time/residue: 1.0500 time to fit residues: 258.1516 Evaluate side-chains 214 residues out of total 2509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain B residue 171 ARG Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 369 CYS Chi-restraints excluded: chain C residue 1 THR Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 31 HIS Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 218 GLU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 57 SER Chi-restraints excluded: chain J residue 155 ILE Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 218 GLU Chi-restraints excluded: chain K residue 150 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 213 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 218 optimal weight: 20.0000 chunk 178 optimal weight: 0.0980 chunk 153 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 250 optimal weight: 3.9990 chunk 189 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 13 optimal weight: 0.3980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.130960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.090898 restraints weight = 90586.055| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.31 r_work: 0.2848 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22868 Z= 0.096 Angle : 0.486 9.595 31233 Z= 0.248 Chirality : 0.043 0.157 3623 Planarity : 0.004 0.087 3833 Dihedral : 4.235 23.997 3285 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.96 % Allowed : 15.98 % Favored : 83.06 % 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: 0.28 (0.16), residues: 2719 helix: 2.12 (0.20), residues: 704 sheet: -0.25 (0.18), residues: 759 loop : -0.60 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 328 TYR 0.022 0.001 TYR K 152 PHE 0.014 0.001 PHE J 214 TRP 0.010 0.001 TRP B 317 HIS 0.003 0.000 HIS E 297 Details of bonding type rmsd covalent geometry : bond 0.00219 (22837) covalent geometry : angle 0.48199 (31156) SS BOND : bond 0.00540 ( 16) SS BOND : angle 1.07236 ( 32) hydrogen bonds : bond 0.03694 ( 988) hydrogen bonds : angle 4.47277 ( 2982) link_BETA1-4 : bond 0.00345 ( 4) link_BETA1-4 : angle 1.63823 ( 12) link_NAG-ASN : bond 0.00147 ( 11) link_NAG-ASN : angle 1.58180 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13946.91 seconds wall clock time: 236 minutes 47.41 seconds (14207.41 seconds total)