Starting phenix.real_space_refine on Tue Aug 26 20:27:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dmt_47015/08_2025/9dmt_47015_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dmt_47015/08_2025/9dmt_47015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dmt_47015/08_2025/9dmt_47015_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dmt_47015/08_2025/9dmt_47015_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dmt_47015/08_2025/9dmt_47015.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dmt_47015/08_2025/9dmt_47015.map" } resolution = 2.18 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 87 5.16 5 C 13313 2.51 5 N 3253 2.21 5 O 3807 1.98 5 H 19744 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s 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: 40208 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 6433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6433 Classifications: {'peptide': 399} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 378} Chain breaks: 1 Chain: "C" Number of atoms: 6486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 6486 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 380} Chain breaks: 1 Chain: "E" Number of atoms: 6575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6575 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 379} Chain breaks: 3 Chain: "D" Number of atoms: 7053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 7053 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 402} Chain breaks: 1 Chain: "B" Number of atoms: 6480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6480 Classifications: {'peptide': 411} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 387} Chain breaks: 1 Chain: "F" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3315 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 210} Chain breaks: 1 Chain: "G" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3171 Classifications: {'peptide': 208} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 197} Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {'CLR': 2, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'CLR': 2, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.88, per 1000 atoms: 0.17 Number of scatterers: 40208 At special positions: 0 Unit cell: (100.045, 108.46, 239.36, 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 87 16.00 P 4 15.00 O 3807 8.00 N 3253 7.00 C 13313 6.00 H 19744 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.06 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 130 " - pdb=" SG CYS D 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 470 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 127 " distance=2.03 Simple disulfide: pdb=" SG CYS F 187 " - pdb=" SG CYS F 243 " distance=2.04 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 212 " distance=1.71 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 ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 6 " " MAN K 4 " - " MAN K 5 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 5 " 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 J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG B 501 " - " ASN B 66 " " NAG D 501 " - " ASN D 76 " " NAG H 1 " - " ASN A 141 " " NAG I 1 " - " ASN C 141 " " NAG J 1 " - " ASN E 141 " " NAG K 1 " - " ASN D 143 " " NAG L 1 " - " ASN B 141 " Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4714 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 30 sheets defined 39.2% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.991A pdb=" N GLY A 73 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.608A pdb=" N LYS A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 218 through 230 removed outlier: 3.852A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 264 removed outlier: 3.804A pdb=" N LEU A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 319 through 324 removed outlier: 4.085A pdb=" N ILE A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 436 removed outlier: 3.599A pdb=" N TRP A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLY A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 removed outlier: 3.504A pdb=" N PHE C 12 " --> pdb=" O VAL C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.918A pdb=" N GLY C 73 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 218 through 231 removed outlier: 3.936A pdb=" N GLY C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 235 Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'C' and resid 241 through 264 removed outlier: 3.970A pdb=" N LEU C 258 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 300 Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.694A pdb=" N ASP C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.751A pdb=" N ASN C 322 " --> pdb=" O ASP C 318 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C 323 " --> pdb=" O THR C 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 318 through 323' Processing helix chain 'C' and resid 369 through 435 removed outlier: 3.538A pdb=" N PHE C 426 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLY C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ARG C 429 " --> pdb=" O VAL C 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.153A pdb=" N ASP E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 222 through 229 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 251 Processing helix chain 'E' and resid 252 through 273 removed outlier: 4.133A pdb=" N ASP E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 311 Processing helix chain 'E' and resid 320 through 329 removed outlier: 3.516A pdb=" N HIS E 329 " --> pdb=" O GLN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.761A pdb=" N TYR E 334 " --> pdb=" O LYS E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 469 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.557A pdb=" N GLY D 254 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 276 removed outlier: 3.553A pdb=" N VAL D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 314 Processing helix chain 'D' and resid 323 through 332 removed outlier: 3.720A pdb=" N GLU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 409 through 473 Proline residue: D 416 - end of helix Proline residue: D 458 - end of helix removed outlier: 3.811A pdb=" N GLY D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR D 473 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.551A pdb=" N ARG B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 66 Processing helix chain 'B' and resid 68 through 73 removed outlier: 4.164A pdb=" N GLY B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 247 through 250 Processing helix chain 'B' and resid 251 through 272 removed outlier: 3.779A pdb=" N GLN B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 310 Processing helix chain 'B' and resid 319 through 328 removed outlier: 3.547A pdb=" N ARG B 323 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.944A pdb=" N ARG B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 459 removed outlier: 3.576A pdb=" N TRP B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 63 removed outlier: 3.519A pdb=" N TYR F 63 " --> pdb=" O PHE F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 96 removed outlier: 3.644A pdb=" N LYS F 96 " --> pdb=" O ASP F 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 93 through 96' Processing helix chain 'F' and resid 118 through 122 Processing helix chain 'F' and resid 132 through 134 No H-bonds generated for 'chain 'F' and resid 132 through 134' Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 232 through 236 removed outlier: 4.088A pdb=" N SER F 235 " --> pdb=" O PRO F 232 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU F 236 " --> pdb=" O SER F 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 232 through 236' Processing helix chain 'G' and resid 98 through 102 removed outlier: 3.802A pdb=" N PHE G 102 " --> pdb=" O PRO G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 145 removed outlier: 3.607A pdb=" N SER G 145 " --> pdb=" O GLU G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 207 removed outlier: 3.939A pdb=" N HIS G 207 " --> pdb=" O ASP G 203 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.067A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.067A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 49 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL A 43 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR A 51 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ARG A 55 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU A 37 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS A 57 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU A 35 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLN A 59 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N VAL A 33 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N VAL A 61 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL A 31 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.755A pdb=" N THR A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A 199 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N THR A 196 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N THR A 189 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR A 198 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER A 187 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP A 200 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR A 202 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLY A 183 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N HIS A 204 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER A 181 " --> pdb=" O HIS A 204 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A 206 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.204A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.204A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE C 49 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL C 43 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR C 51 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG C 55 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LEU C 37 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS C 57 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU C 35 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN C 59 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL C 33 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N VAL C 61 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL C 31 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.739A pdb=" N THR C 148 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU C 199 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 180 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN C 208 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ILE C 178 " --> pdb=" O GLN C 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.004A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.004A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU E 49 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU E 43 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER E 51 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR E 55 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU E 37 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP E 57 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LEU E 35 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N GLU E 59 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL E 33 " --> pdb=" O GLU E 59 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR E 61 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL E 31 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 11.128A pdb=" N TYR E 63 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 13.357A pdb=" N VAL E 29 " --> pdb=" O TYR E 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 92 removed outlier: 6.880A pdb=" N ILE E 217 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.795A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLY D 116 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.795A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLY D 116 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR D 51 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER D 44 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR D 53 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU D 42 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASN D 55 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR D 63 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP D 32 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL D 31 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SER D 161 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL D 33 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 93 through 94 removed outlier: 6.864A pdb=" N ILE D 220 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 93 through 94 Processing sheet with id=AB6, first strand: chain 'D' and resid 164 through 167 Processing sheet with id=AB7, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.634A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.634A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR B 49 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU B 43 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR B 51 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TRP B 55 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU B 37 " --> pdb=" O TRP B 55 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLY B 57 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL B 35 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP B 59 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU B 33 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N GLN B 61 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ILE B 31 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.246A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE B 215 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.246A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 34 through 38 Processing sheet with id=AC3, first strand: chain 'F' and resid 41 through 43 removed outlier: 6.406A pdb=" N GLY F 41 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TRP F 64 " --> pdb=" O ASP F 130 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N MET F 65 " --> pdb=" O HIS F 81 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N HIS F 81 " --> pdb=" O MET F 65 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP F 67 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 41 through 43 removed outlier: 6.406A pdb=" N GLY F 41 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG F 129 " --> pdb=" O PRO F 149 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 167 through 171 removed outlier: 6.025A pdb=" N TYR F 223 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 167 through 171 removed outlier: 6.025A pdb=" N TYR F 223 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 198 through 200 Processing sheet with id=AC8, first strand: chain 'G' and resid 23 through 26 Processing sheet with id=AC9, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.674A pdb=" N LEU G 30 " --> pdb=" O GLU G 123 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU G 52 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR G 68 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP G 54 " --> pdb=" O LEU G 66 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.674A pdb=" N LEU G 30 " --> pdb=" O GLU G 123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 132 through 136 removed outlier: 6.000A pdb=" N TYR G 191 " --> pdb=" O ASN G 156 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 164 through 168 1113 hydrogen bonds defined for protein. 3117 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.31 Time building geometry restraints manager: 5.22 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: 19723 1.04 - 1.23: 875 1.23 - 1.43: 7834 1.43 - 1.63: 12162 1.63 - 1.83: 135 Bond restraints: 40729 Sorted by residual: bond pdb=" NZ LYS C 13 " pdb=" HZ1 LYS C 13 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS G 64 " pdb=" HZ1 LYS G 64 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS E 46 " pdb=" HZ1 LYS E 46 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS F 248 " pdb=" HZ3 LYS F 248 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS C 13 " pdb=" HZ2 LYS C 13 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 40724 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.46: 73445 12.46 - 24.91: 2 24.91 - 37.37: 1 37.37 - 49.82: 1 49.82 - 62.28: 4 Bond angle restraints: 73453 Sorted by residual: angle pdb=" CA LEU E 407 " pdb=" N LEU E 407 " pdb=" H LEU E 407 " ideal model delta sigma weight residual 114.00 176.28 -62.28 3.00e+00 1.11e-01 4.31e+02 angle pdb=" CA LEU C 366 " pdb=" N LEU C 366 " pdb=" H LEU C 366 " ideal model delta sigma weight residual 114.00 168.17 -54.17 3.00e+00 1.11e-01 3.26e+02 angle pdb=" CA ALA B 397 " pdb=" N ALA B 397 " pdb=" H ALA B 397 " ideal model delta sigma weight residual 114.00 166.14 -52.14 3.00e+00 1.11e-01 3.02e+02 angle pdb=" CA LYS A 368 " pdb=" N LYS A 368 " pdb=" H LYS A 368 " ideal model delta sigma weight residual 114.00 165.57 -51.57 3.00e+00 1.11e-01 2.96e+02 angle pdb=" CA GLY E 168 " pdb=" N GLY E 168 " pdb=" H GLY E 168 " ideal model delta sigma weight residual 114.00 153.65 -39.65 3.00e+00 1.11e-01 1.75e+02 ... (remaining 73448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 19414 35.70 - 71.41: 536 71.41 - 107.11: 84 107.11 - 142.82: 12 142.82 - 178.52: 1 Dihedral angle restraints: 20047 sinusoidal: 11292 harmonic: 8755 Sorted by residual: dihedral pdb=" C29 POV E 502 " pdb="C210 POV E 502 " pdb="C211 POV E 502 " pdb="C212 POV E 502 " ideal model delta sinusoidal sigma weight residual 112.25 -69.23 -178.52 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C37 POV E 502 " pdb=" C38 POV E 502 " pdb=" C39 POV E 502 " pdb="C310 POV E 502 " ideal model delta sinusoidal sigma weight residual -179.61 -47.81 -131.80 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C ILE E 106 " pdb=" N ILE E 106 " pdb=" CA ILE E 106 " pdb=" CB ILE E 106 " ideal model delta harmonic sigma weight residual -122.00 -132.41 10.41 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 20044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 3189 0.105 - 0.210: 187 0.210 - 0.314: 6 0.314 - 0.419: 2 0.419 - 0.524: 1 Chirality restraints: 3385 Sorted by residual: chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 76 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.86e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 141 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 66 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 3382 not shown) Planarity restraints: 5829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV E 502 " 0.146 2.00e-02 2.50e+03 1.52e-01 2.32e+02 pdb=" C29 POV E 502 " -0.127 2.00e-02 2.50e+03 pdb="C210 POV E 502 " -0.176 2.00e-02 2.50e+03 pdb="C211 POV E 502 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 117 " -0.480 9.50e-02 1.11e+02 1.60e-01 2.80e+01 pdb=" NE ARG E 117 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG E 117 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG E 117 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 117 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG E 117 " 0.019 2.00e-02 2.50e+03 pdb="HH12 ARG E 117 " -0.009 2.00e-02 2.50e+03 pdb="HH21 ARG E 117 " 0.012 2.00e-02 2.50e+03 pdb="HH22 ARG E 117 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 160 " -0.475 9.50e-02 1.11e+02 1.58e-01 2.67e+01 pdb=" NE ARG G 160 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG G 160 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 160 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 160 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG G 160 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG G 160 " -0.004 2.00e-02 2.50e+03 pdb="HH21 ARG G 160 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG G 160 " -0.008 2.00e-02 2.50e+03 ... (remaining 5826 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.83: 73 1.83 - 2.52: 30676 2.52 - 3.21: 122451 3.21 - 3.91: 165056 3.91 - 4.60: 257580 Nonbonded interactions: 575836 Sorted by model distance: nonbonded pdb=" HH TYR F 143 " pdb=" HE1 TRP G 114 " model vdw 1.137 2.100 nonbonded pdb="HH21 ARG G 126 " pdb="HG22 THR G 190 " model vdw 1.252 2.270 nonbonded pdb=" HH TYR E 15 " pdb=" H TRP E 86 " model vdw 1.268 2.100 nonbonded pdb=" HE1 MET A 308 " pdb="HG12 VAL A 312 " model vdw 1.278 2.440 nonbonded pdb="HD22 ASN B 301 " pdb=" HB3 CYS B 438 " model vdw 1.357 2.270 ... (remaining 575831 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 436) selection = (chain 'C' and (resid 1 through 330 or resid 369 through 436)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' } 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: 6.000 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: 0.240 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 39.190 Find NCS groups from input model: 0.440 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:9.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 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 : 0.006 0.324 21022 Z= 0.279 Angle : 0.868 12.027 28722 Z= 0.431 Chirality : 0.052 0.524 3385 Planarity : 0.008 0.205 3497 Dihedral : 17.311 178.521 8397 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.20 % Favored : 97.76 % Rotamer: Outliers : 0.45 % Allowed : 10.89 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.43 % 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: 1.05 (0.17), residues: 2450 helix: 2.31 (0.18), residues: 791 sheet: 0.04 (0.20), residues: 602 loop : -0.06 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A 313 TYR 0.015 0.001 TYR F 143 PHE 0.024 0.002 PHE C 284 TRP 0.013 0.001 TRP G 51 HIS 0.017 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00543 (20985) covalent geometry : angle 0.85539 (28620) SS BOND : bond 0.10847 ( 9) SS BOND : angle 1.39676 ( 18) hydrogen bonds : bond 0.11498 ( 1005) hydrogen bonds : angle 5.39971 ( 3117) link_ALPHA1-3 : bond 0.00548 ( 6) link_ALPHA1-3 : angle 1.51233 ( 18) link_ALPHA1-6 : bond 0.00381 ( 5) link_ALPHA1-6 : angle 1.81114 ( 15) link_BETA1-4 : bond 0.00248 ( 10) link_BETA1-4 : angle 2.68353 ( 30) link_NAG-ASN : bond 0.00452 ( 7) link_NAG-ASN : angle 4.05074 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 238 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ASN cc_start: 0.7755 (m-40) cc_final: 0.7387 (m110) REVERT: E 336 ARG cc_start: 0.8042 (mpt180) cc_final: 0.7821 (mmt90) REVERT: B 422 GLU cc_start: 0.6739 (mm-30) cc_final: 0.6510 (mp0) outliers start: 10 outliers final: 4 residues processed: 244 average time/residue: 1.5332 time to fit residues: 420.1508 Evaluate side-chains 219 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 215 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain G residue 24 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 322 ASN A 393 ASN A 408 HIS C 111 GLN C 306 HIS E 131 GLN E 325 GLN D 491 GLN B 95 ASN B 301 ASN B 417 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.149832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103478 restraints weight = 60216.843| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.71 r_work: 0.3111 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21022 Z= 0.134 Angle : 0.581 10.135 28722 Z= 0.289 Chirality : 0.044 0.263 3385 Planarity : 0.005 0.060 3497 Dihedral : 12.233 173.680 3753 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.84 % Favored : 98.12 % Rotamer: Outliers : 1.43 % Allowed : 10.71 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.43 % 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: 1.31 (0.17), residues: 2450 helix: 2.56 (0.18), residues: 803 sheet: 0.08 (0.20), residues: 620 loop : 0.10 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 313 TYR 0.011 0.001 TYR F 143 PHE 0.015 0.001 PHE C 284 TRP 0.010 0.001 TRP G 114 HIS 0.006 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00292 (20985) covalent geometry : angle 0.56621 (28620) SS BOND : bond 0.00873 ( 9) SS BOND : angle 2.53948 ( 18) hydrogen bonds : bond 0.04694 ( 1005) hydrogen bonds : angle 4.54250 ( 3117) link_ALPHA1-3 : bond 0.00658 ( 6) link_ALPHA1-3 : angle 2.47659 ( 18) link_ALPHA1-6 : bond 0.00611 ( 5) link_ALPHA1-6 : angle 1.76442 ( 15) link_BETA1-4 : bond 0.00327 ( 10) link_BETA1-4 : angle 2.29468 ( 30) link_NAG-ASN : bond 0.00128 ( 7) link_NAG-ASN : angle 2.13338 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.6931 (tpt) REVERT: A 310 ASN cc_start: 0.7735 (m-40) cc_final: 0.7416 (m110) REVERT: C 420 ILE cc_start: 0.8172 (mt) cc_final: 0.7920 (mm) REVERT: E 336 ARG cc_start: 0.8194 (mpt180) cc_final: 0.7954 (mmt90) REVERT: B 34 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8596 (ttmm) REVERT: B 410 VAL cc_start: 0.7392 (t) cc_final: 0.6976 (m) REVERT: B 422 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6501 (mp0) REVERT: G 46 GLN cc_start: 0.5719 (pm20) cc_final: 0.5496 (pm20) outliers start: 32 outliers final: 16 residues processed: 241 average time/residue: 1.5969 time to fit residues: 433.2165 Evaluate side-chains 232 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain E residue 1 SER Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 74 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 188 optimal weight: 2.9990 chunk 162 optimal weight: 0.2980 chunk 152 optimal weight: 0.3980 chunk 121 optimal weight: 0.7980 chunk 171 optimal weight: 0.5980 chunk 202 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN C 393 ASN C 394 ASN E 131 GLN E 325 GLN D 491 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.150543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104459 restraints weight = 60154.747| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.71 r_work: 0.3125 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21022 Z= 0.105 Angle : 0.521 5.869 28722 Z= 0.260 Chirality : 0.043 0.226 3385 Planarity : 0.004 0.058 3497 Dihedral : 10.495 159.975 3750 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.88 % Favored : 98.08 % Rotamer: Outliers : 1.20 % Allowed : 10.00 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.43 % 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: 1.56 (0.17), residues: 2450 helix: 2.77 (0.18), residues: 803 sheet: 0.26 (0.20), residues: 602 loop : 0.20 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 313 TYR 0.011 0.001 TYR D 119 PHE 0.014 0.001 PHE C 284 TRP 0.009 0.001 TRP A 60 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00226 (20985) covalent geometry : angle 0.51181 (28620) SS BOND : bond 0.00366 ( 9) SS BOND : angle 1.60009 ( 18) hydrogen bonds : bond 0.04216 ( 1005) hydrogen bonds : angle 4.25749 ( 3117) link_ALPHA1-3 : bond 0.01019 ( 6) link_ALPHA1-3 : angle 1.46706 ( 18) link_ALPHA1-6 : bond 0.00774 ( 5) link_ALPHA1-6 : angle 1.63971 ( 15) link_BETA1-4 : bond 0.00470 ( 10) link_BETA1-4 : angle 1.75668 ( 30) link_NAG-ASN : bond 0.00130 ( 7) link_NAG-ASN : angle 1.81248 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 ASN cc_start: 0.7752 (m-40) cc_final: 0.7426 (m110) REVERT: C 4 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: C 407 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7915 (t0) REVERT: E 336 ARG cc_start: 0.8133 (mpt180) cc_final: 0.7894 (mmt90) REVERT: D 72 GLU cc_start: 0.8025 (pm20) cc_final: 0.7820 (pm20) REVERT: D 186 GLU cc_start: 0.7834 (tp30) cc_final: 0.7571 (tp30) REVERT: B 34 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8573 (ttmm) REVERT: B 422 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6576 (mp0) REVERT: F 104 ASP cc_start: 0.7446 (t0) cc_final: 0.7239 (t0) REVERT: F 155 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7694 (tt) REVERT: G 46 GLN cc_start: 0.5649 (pm20) cc_final: 0.5401 (pm20) REVERT: G 121 LYS cc_start: 0.7220 (ttmm) cc_final: 0.7007 (tttp) outliers start: 27 outliers final: 13 residues processed: 240 average time/residue: 1.6440 time to fit residues: 442.6020 Evaluate side-chains 233 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 216 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 74 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 193 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN E 131 GLN E 325 GLN E 427 GLN D 164 GLN B 310 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.144584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098129 restraints weight = 60154.959| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.68 r_work: 0.3031 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 21022 Z= 0.275 Angle : 0.648 9.342 28722 Z= 0.330 Chirality : 0.048 0.277 3385 Planarity : 0.006 0.056 3497 Dihedral : 11.263 172.961 3750 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.67 % Rotamer: Outliers : 1.56 % Allowed : 9.77 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.32 (0.17), residues: 2450 helix: 2.35 (0.17), residues: 805 sheet: 0.33 (0.20), residues: 615 loop : 0.13 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 313 TYR 0.013 0.002 TYR A 72 PHE 0.023 0.002 PHE E 267 TRP 0.019 0.002 TRP D 176 HIS 0.009 0.002 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00645 (20985) covalent geometry : angle 0.63202 (28620) SS BOND : bond 0.00615 ( 9) SS BOND : angle 2.73320 ( 18) hydrogen bonds : bond 0.05477 ( 1005) hydrogen bonds : angle 4.58751 ( 3117) link_ALPHA1-3 : bond 0.00792 ( 6) link_ALPHA1-3 : angle 2.11661 ( 18) link_ALPHA1-6 : bond 0.00719 ( 5) link_ALPHA1-6 : angle 1.59475 ( 15) link_BETA1-4 : bond 0.00686 ( 10) link_BETA1-4 : angle 2.92338 ( 30) link_NAG-ASN : bond 0.00749 ( 7) link_NAG-ASN : angle 2.31326 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7252 (tpt) REVERT: C 4 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: C 420 ILE cc_start: 0.8178 (mt) cc_final: 0.7965 (mm) REVERT: D 60 HIS cc_start: 0.9453 (OUTLIER) cc_final: 0.9203 (m90) REVERT: D 460 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7839 (mtp) REVERT: B 34 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8641 (ttmm) REVERT: F 34 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8035 (tt0) REVERT: G 51 TRP cc_start: 0.8609 (m-90) cc_final: 0.8382 (m-90) outliers start: 35 outliers final: 19 residues processed: 244 average time/residue: 1.6594 time to fit residues: 453.8716 Evaluate side-chains 248 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 82 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 76 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 225 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 184 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN C 394 ASN E 131 GLN E 325 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.145901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.100127 restraints weight = 60689.867| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.66 r_work: 0.3119 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21022 Z= 0.173 Angle : 0.564 8.197 28722 Z= 0.287 Chirality : 0.044 0.198 3385 Planarity : 0.005 0.045 3497 Dihedral : 10.693 173.551 3750 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.16 % Favored : 97.80 % Rotamer: Outliers : 1.38 % Allowed : 10.00 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.43 % 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: 1.39 (0.17), residues: 2450 helix: 2.45 (0.17), residues: 805 sheet: 0.40 (0.20), residues: 612 loop : 0.10 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 313 TYR 0.011 0.001 TYR D 434 PHE 0.019 0.002 PHE C 284 TRP 0.011 0.001 TRP B 55 HIS 0.005 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00382 (20985) covalent geometry : angle 0.55127 (28620) SS BOND : bond 0.00428 ( 9) SS BOND : angle 2.24081 ( 18) hydrogen bonds : bond 0.04847 ( 1005) hydrogen bonds : angle 4.42422 ( 3117) link_ALPHA1-3 : bond 0.00752 ( 6) link_ALPHA1-3 : angle 1.59263 ( 18) link_ALPHA1-6 : bond 0.00800 ( 5) link_ALPHA1-6 : angle 1.80321 ( 15) link_BETA1-4 : bond 0.00480 ( 10) link_BETA1-4 : angle 2.35518 ( 30) link_NAG-ASN : bond 0.00270 ( 7) link_NAG-ASN : angle 1.87873 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8167 (tp) REVERT: C 4 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: C 420 ILE cc_start: 0.8137 (mt) cc_final: 0.7921 (mm) REVERT: D 60 HIS cc_start: 0.9418 (OUTLIER) cc_final: 0.9178 (m90) REVERT: D 460 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7832 (mtp) REVERT: B 34 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8640 (ttmm) REVERT: B 422 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6708 (mp0) REVERT: F 34 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8061 (tt0) REVERT: F 155 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7702 (tt) outliers start: 31 outliers final: 15 residues processed: 236 average time/residue: 1.7196 time to fit residues: 454.4041 Evaluate side-chains 241 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 74 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 156 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 HIS C 393 ASN E 131 GLN E 325 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.145056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.099062 restraints weight = 60859.604| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.66 r_work: 0.3106 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21022 Z= 0.206 Angle : 0.590 7.354 28722 Z= 0.300 Chirality : 0.045 0.212 3385 Planarity : 0.005 0.060 3497 Dihedral : 10.670 178.327 3750 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.20 % Favored : 97.76 % Rotamer: Outliers : 1.74 % Allowed : 9.86 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.36 (0.17), residues: 2450 helix: 2.39 (0.17), residues: 805 sheet: 0.42 (0.20), residues: 614 loop : 0.10 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 313 TYR 0.012 0.002 TYR A 72 PHE 0.022 0.002 PHE C 284 TRP 0.014 0.002 TRP D 176 HIS 0.006 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00471 (20985) covalent geometry : angle 0.57574 (28620) SS BOND : bond 0.00506 ( 9) SS BOND : angle 2.17713 ( 18) hydrogen bonds : bond 0.05074 ( 1005) hydrogen bonds : angle 4.47634 ( 3117) link_ALPHA1-3 : bond 0.00640 ( 6) link_ALPHA1-3 : angle 1.76307 ( 18) link_ALPHA1-6 : bond 0.00837 ( 5) link_ALPHA1-6 : angle 2.00183 ( 15) link_BETA1-4 : bond 0.00553 ( 10) link_BETA1-4 : angle 2.66285 ( 30) link_NAG-ASN : bond 0.00473 ( 7) link_NAG-ASN : angle 2.12062 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8195 (tp) REVERT: A 308 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7417 (tpt) REVERT: C 4 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: C 377 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7056 (mp0) REVERT: C 420 ILE cc_start: 0.8117 (mt) cc_final: 0.7892 (mm) REVERT: D 60 HIS cc_start: 0.9428 (OUTLIER) cc_final: 0.9190 (m90) REVERT: D 186 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7642 (tp30) REVERT: D 332 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: D 460 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7849 (mtp) REVERT: B 34 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8653 (ttmm) REVERT: F 155 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7700 (tt) outliers start: 39 outliers final: 21 residues processed: 243 average time/residue: 1.6640 time to fit residues: 454.4112 Evaluate side-chains 252 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain D residue 60 HIS Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 82 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 82 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 147 optimal weight: 0.0870 chunk 202 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN C 394 ASN E 131 GLN E 325 GLN D 491 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.145601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.099737 restraints weight = 60707.476| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.70 r_work: 0.3113 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21022 Z= 0.168 Angle : 0.559 6.340 28722 Z= 0.285 Chirality : 0.044 0.198 3385 Planarity : 0.005 0.080 3497 Dihedral : 10.386 178.081 3750 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.37 % Favored : 97.59 % Rotamer: Outliers : 1.56 % Allowed : 10.13 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.41 (0.17), residues: 2450 helix: 2.47 (0.18), residues: 805 sheet: 0.41 (0.20), residues: 609 loop : 0.12 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 313 TYR 0.011 0.001 TYR D 434 PHE 0.020 0.002 PHE C 284 TRP 0.010 0.001 TRP D 176 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00376 (20985) covalent geometry : angle 0.54673 (28620) SS BOND : bond 0.00397 ( 9) SS BOND : angle 1.85770 ( 18) hydrogen bonds : bond 0.04826 ( 1005) hydrogen bonds : angle 4.40861 ( 3117) link_ALPHA1-3 : bond 0.00686 ( 6) link_ALPHA1-3 : angle 1.59730 ( 18) link_ALPHA1-6 : bond 0.00870 ( 5) link_ALPHA1-6 : angle 2.06316 ( 15) link_BETA1-4 : bond 0.00453 ( 10) link_BETA1-4 : angle 2.39910 ( 30) link_NAG-ASN : bond 0.00293 ( 7) link_NAG-ASN : angle 1.92233 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8171 (tp) REVERT: A 308 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7537 (tpt) REVERT: C 4 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: C 377 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7038 (mp0) REVERT: C 420 ILE cc_start: 0.8102 (mt) cc_final: 0.7879 (mm) REVERT: D 186 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7628 (tp30) REVERT: D 332 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: D 460 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7820 (mtp) REVERT: B 34 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8639 (ttmm) REVERT: B 273 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.7939 (mtpp) REVERT: B 422 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6805 (mp0) REVERT: F 155 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7691 (tt) outliers start: 35 outliers final: 22 residues processed: 239 average time/residue: 1.7230 time to fit residues: 461.6417 Evaluate side-chains 252 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 221 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 82 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 52 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN E 131 GLN E 325 GLN D 60 HIS D 491 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.146250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.100303 restraints weight = 60735.628| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.68 r_work: 0.3126 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21022 Z= 0.145 Angle : 0.537 4.958 28722 Z= 0.273 Chirality : 0.043 0.208 3385 Planarity : 0.004 0.069 3497 Dihedral : 9.879 171.114 3750 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.29 % Favored : 97.67 % Rotamer: Outliers : 1.56 % Allowed : 10.17 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.50 (0.17), residues: 2450 helix: 2.58 (0.18), residues: 805 sheet: 0.44 (0.20), residues: 609 loop : 0.14 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 43 TYR 0.011 0.001 TYR D 434 PHE 0.019 0.001 PHE C 284 TRP 0.010 0.001 TRP B 55 HIS 0.004 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00322 (20985) covalent geometry : angle 0.52601 (28620) SS BOND : bond 0.00367 ( 9) SS BOND : angle 1.51415 ( 18) hydrogen bonds : bond 0.04598 ( 1005) hydrogen bonds : angle 4.32084 ( 3117) link_ALPHA1-3 : bond 0.00705 ( 6) link_ALPHA1-3 : angle 1.58595 ( 18) link_ALPHA1-6 : bond 0.00889 ( 5) link_ALPHA1-6 : angle 2.07412 ( 15) link_BETA1-4 : bond 0.00403 ( 10) link_BETA1-4 : angle 2.24178 ( 30) link_NAG-ASN : bond 0.00239 ( 7) link_NAG-ASN : angle 1.90077 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 LEU cc_start: 0.8429 (mp) cc_final: 0.8095 (mp) REVERT: C 4 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: C 377 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7039 (mp0) REVERT: C 420 ILE cc_start: 0.8077 (mt) cc_final: 0.7855 (mm) REVERT: D 28 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: D 186 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7619 (tp30) REVERT: D 332 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: B 34 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8641 (ttmm) REVERT: B 422 GLU cc_start: 0.7356 (mm-30) cc_final: 0.6783 (mp0) REVERT: F 155 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7722 (tt) outliers start: 35 outliers final: 20 residues processed: 239 average time/residue: 1.7080 time to fit residues: 459.4278 Evaluate side-chains 243 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 82 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 136 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 216 optimal weight: 0.7980 chunk 237 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN C 394 ASN E 131 GLN E 325 GLN D 491 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.144336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.097581 restraints weight = 60466.311| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.65 r_work: 0.3051 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21022 Z= 0.177 Angle : 0.563 5.806 28722 Z= 0.286 Chirality : 0.044 0.200 3385 Planarity : 0.005 0.077 3497 Dihedral : 9.867 159.229 3750 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.33 % Favored : 97.63 % Rotamer: Outliers : 1.34 % Allowed : 10.58 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.47 (0.17), residues: 2450 helix: 2.54 (0.18), residues: 805 sheet: 0.43 (0.20), residues: 609 loop : 0.13 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 313 TYR 0.011 0.001 TYR D 434 PHE 0.021 0.002 PHE C 284 TRP 0.012 0.001 TRP D 176 HIS 0.009 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00402 (20985) covalent geometry : angle 0.55016 (28620) SS BOND : bond 0.00436 ( 9) SS BOND : angle 1.78289 ( 18) hydrogen bonds : bond 0.04814 ( 1005) hydrogen bonds : angle 4.37537 ( 3117) link_ALPHA1-3 : bond 0.00635 ( 6) link_ALPHA1-3 : angle 1.62128 ( 18) link_ALPHA1-6 : bond 0.00856 ( 5) link_ALPHA1-6 : angle 2.04591 ( 15) link_BETA1-4 : bond 0.00487 ( 10) link_BETA1-4 : angle 2.43265 ( 30) link_NAG-ASN : bond 0.00378 ( 7) link_NAG-ASN : angle 1.98452 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: C 179 LYS cc_start: 0.8596 (mtpt) cc_final: 0.8346 (mmpt) REVERT: C 420 ILE cc_start: 0.8071 (mt) cc_final: 0.7844 (mm) REVERT: D 186 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7584 (tp30) REVERT: D 332 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: B 34 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8612 (ttmm) REVERT: B 273 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.7946 (mtpp) REVERT: F 155 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7694 (tt) REVERT: G 46 GLN cc_start: 0.5767 (pm20) cc_final: 0.5494 (pm20) outliers start: 30 outliers final: 22 residues processed: 240 average time/residue: 1.6375 time to fit residues: 440.5628 Evaluate side-chains 244 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 82 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 60 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 181 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 183 optimal weight: 0.3980 chunk 178 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN E 131 GLN E 325 GLN D 491 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.146544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.100640 restraints weight = 60814.253| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.68 r_work: 0.3131 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21022 Z= 0.132 Angle : 0.529 4.753 28722 Z= 0.269 Chirality : 0.043 0.210 3385 Planarity : 0.004 0.061 3497 Dihedral : 9.406 144.591 3750 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.20 % Favored : 97.76 % Rotamer: Outliers : 1.20 % Allowed : 10.84 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.56 (0.17), residues: 2450 helix: 2.66 (0.18), residues: 805 sheet: 0.46 (0.20), residues: 608 loop : 0.17 (0.20), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 313 TYR 0.011 0.001 TYR D 434 PHE 0.017 0.001 PHE C 284 TRP 0.010 0.001 TRP B 55 HIS 0.006 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00290 (20985) covalent geometry : angle 0.51867 (28620) SS BOND : bond 0.00347 ( 9) SS BOND : angle 1.38674 ( 18) hydrogen bonds : bond 0.04480 ( 1005) hydrogen bonds : angle 4.27162 ( 3117) link_ALPHA1-3 : bond 0.00689 ( 6) link_ALPHA1-3 : angle 1.55831 ( 18) link_ALPHA1-6 : bond 0.00932 ( 5) link_ALPHA1-6 : angle 2.04135 ( 15) link_BETA1-4 : bond 0.00398 ( 10) link_BETA1-4 : angle 2.14305 ( 30) link_NAG-ASN : bond 0.00185 ( 7) link_NAG-ASN : angle 1.83976 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4900 Ramachandran restraints generated. 2450 Oldfield, 0 Emsley, 2450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 LEU cc_start: 0.8417 (mp) cc_final: 0.8076 (mp) REVERT: C 4 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: C 179 LYS cc_start: 0.8576 (mtpt) cc_final: 0.8356 (mmpt) REVERT: C 420 ILE cc_start: 0.8065 (mt) cc_final: 0.7844 (mm) REVERT: D 49 GLU cc_start: 0.8475 (mp0) cc_final: 0.8219 (mp0) REVERT: B 422 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6809 (mp0) REVERT: F 155 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7736 (tt) REVERT: G 46 GLN cc_start: 0.5775 (pm20) cc_final: 0.5506 (pm20) outliers start: 27 outliers final: 21 residues processed: 241 average time/residue: 1.3672 time to fit residues: 371.1493 Evaluate side-chains 246 residues out of total 2241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 475 ASP Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain F residue 81 HIS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 82 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 16 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 232 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN C 394 ASN E 131 GLN E 325 GLN D 491 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.146265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100345 restraints weight = 60908.550| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.69 r_work: 0.3127 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21022 Z= 0.160 Angle : 0.549 5.132 28722 Z= 0.279 Chirality : 0.043 0.201 3385 Planarity : 0.004 0.060 3497 Dihedral : 9.330 119.986 3750 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.33 % Favored : 97.63 % Rotamer: Outliers : 1.20 % Allowed : 10.84 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.54 (0.17), residues: 2450 helix: 2.62 (0.18), residues: 805 sheet: 0.48 (0.20), residues: 610 loop : 0.15 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 313 TYR 0.011 0.001 TYR D 434 PHE 0.019 0.002 PHE C 284 TRP 0.010 0.001 TRP D 176 HIS 0.007 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00363 (20985) covalent geometry : angle 0.53753 (28620) SS BOND : bond 0.00383 ( 9) SS BOND : angle 1.62903 ( 18) hydrogen bonds : bond 0.04668 ( 1005) hydrogen bonds : angle 4.31318 ( 3117) link_ALPHA1-3 : bond 0.00608 ( 6) link_ALPHA1-3 : angle 1.61962 ( 18) link_ALPHA1-6 : bond 0.00861 ( 5) link_ALPHA1-6 : angle 1.96428 ( 15) link_BETA1-4 : bond 0.00460 ( 10) link_BETA1-4 : angle 2.35688 ( 30) link_NAG-ASN : bond 0.00338 ( 7) link_NAG-ASN : angle 1.98956 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18590.39 seconds wall clock time: 314 minutes 44.03 seconds (18884.03 seconds total)