Starting phenix.real_space_refine on Sun Sep 13 10:03:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pds_13342/09_2026/7pds_13342.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pds_13342/09_2026/7pds_13342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7pds_13342/09_2026/7pds_13342.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pds_13342/09_2026/7pds_13342.cif" model { file = "/net/cci-nas-00/data/ceres_data/7pds_13342/09_2026/7pds_13342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pds_13342/09_2026/7pds_13342.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pds_13342/09_2026/7pds_13342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pds_13342/09_2026/7pds_13342.map" } resolution = 3.14 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= 0.004 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 23 5.49 5 Mg 4 5.21 5 S 90 5.16 5 C 14281 2.51 5 N 3871 2.21 5 O 4280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22549 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3746 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 12, 'TRANS': 444} Chain breaks: 1 Chain: "B" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3670 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 13, 'TRANS': 434} Chain breaks: 2 Chain: "C" Number of atoms: 3698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3698 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 13, 'TRANS': 437} Chain breaks: 1 Chain: "D" Number of atoms: 3724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3724 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 13, 'TRANS': 440} Chain breaks: 1 Chain: "E" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3708 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 440} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3709 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 12, 'TRANS': 438} Chain breaks: 3 Chain: "M" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 104 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.51, per 1000 atoms: 0.24 Number of scatterers: 22549 At special positions: 0 Unit cell: (136.12, 118.9, 145.14, 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 90 16.00 P 23 15.00 Mg 4 11.99 O 4280 8.00 N 3871 7.00 C 14281 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.0 seconds 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5118 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 32 sheets defined 47.2% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 33 through 44 Processing helix chain 'A' and resid 79 through 94 Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 117 through 124 Processing helix chain 'A' and resid 136 through 142 Processing helix chain 'A' and resid 147 through 167 Processing helix chain 'A' and resid 185 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.733A pdb=" N LYS A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 231 removed outlier: 3.582A pdb=" N GLN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.617A pdb=" N LEU A 301 " --> pdb=" O PRO A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 319 Processing helix chain 'A' and resid 329 through 343 removed outlier: 3.572A pdb=" N LYS A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 358 removed outlier: 3.801A pdb=" N GLU A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 3.607A pdb=" N VAL A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.814A pdb=" N ILE A 386 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 404 No H-bonds generated for 'chain 'A' and resid 401 through 404' Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 428 through 442 removed outlier: 3.643A pdb=" N LEU A 432 " --> pdb=" O GLN A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 4.686A pdb=" N SER A 470 " --> pdb=" O ASP A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.542A pdb=" N SER B 19 " --> pdb=" O ASP B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 44 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 99 through 114 Processing helix chain 'B' and resid 117 through 124 Processing helix chain 'B' and resid 136 through 142 removed outlier: 3.586A pdb=" N ASP B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 167 removed outlier: 3.825A pdb=" N ARG B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 195 Processing helix chain 'B' and resid 208 through 216 removed outlier: 4.452A pdb=" N GLY B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 230 removed outlier: 3.666A pdb=" N GLN B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 230' Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 302 through 319 Processing helix chain 'B' and resid 322 through 327 removed outlier: 3.792A pdb=" N LEU B 326 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 327 " --> pdb=" O ASP B 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 322 through 327' Processing helix chain 'B' and resid 329 through 343 removed outlier: 3.560A pdb=" N LYS B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 358 removed outlier: 4.396A pdb=" N GLY B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 378 Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 428 through 442 Processing helix chain 'B' and resid 468 through 473 removed outlier: 3.561A pdb=" N LYS B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.543A pdb=" N LEU C 21 " --> pdb=" O LYS C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 44 Processing helix chain 'C' and resid 79 through 94 Processing helix chain 'C' and resid 99 through 114 Processing helix chain 'C' and resid 117 through 124 Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 147 through 167 removed outlier: 3.637A pdb=" N ARG C 151 " --> pdb=" O ASN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 195 Processing helix chain 'C' and resid 208 through 216 removed outlier: 4.405A pdb=" N GLY C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.509A pdb=" N GLN C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 225 through 230' Processing helix chain 'C' and resid 232 through 241 Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.647A pdb=" N LEU C 301 " --> pdb=" O PRO C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 320 removed outlier: 4.214A pdb=" N ASN C 320 " --> pdb=" O TYR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 329 through 343 removed outlier: 3.560A pdb=" N LYS C 338 " --> pdb=" O GLU C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 359 removed outlier: 4.136A pdb=" N GLY C 351 " --> pdb=" O ASP C 347 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 378 Processing helix chain 'C' and resid 401 through 403 No H-bonds generated for 'chain 'C' and resid 401 through 403' Processing helix chain 'C' and resid 412 through 419 Processing helix chain 'C' and resid 430 through 442 Processing helix chain 'C' and resid 467 through 471 removed outlier: 4.556A pdb=" N SER C 470 " --> pdb=" O ASP C 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 21 Processing helix chain 'D' and resid 33 through 43 Processing helix chain 'D' and resid 44 through 48 removed outlier: 3.895A pdb=" N LYS D 48 " --> pdb=" O GLU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 94 Processing helix chain 'D' and resid 99 through 114 Processing helix chain 'D' and resid 117 through 124 Processing helix chain 'D' and resid 136 through 142 Processing helix chain 'D' and resid 147 through 167 Processing helix chain 'D' and resid 185 through 195 Processing helix chain 'D' and resid 208 through 214 Processing helix chain 'D' and resid 225 through 231 removed outlier: 3.504A pdb=" N GLN D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 302 through 320 removed outlier: 3.969A pdb=" N ASN D 320 " --> pdb=" O TYR D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 327 removed outlier: 3.804A pdb=" N LEU D 326 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 343 removed outlier: 3.642A pdb=" N LYS D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 358 removed outlier: 3.751A pdb=" N GLU D 352 " --> pdb=" O ALA D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 369 through 378 removed outlier: 3.659A pdb=" N HIS D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 420 Processing helix chain 'D' and resid 430 through 442 Processing helix chain 'D' and resid 468 through 473 Processing helix chain 'E' and resid 16 through 20 Processing helix chain 'E' and resid 33 through 43 Processing helix chain 'E' and resid 79 through 95 Processing helix chain 'E' and resid 99 through 114 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 136 through 142 Processing helix chain 'E' and resid 147 through 167 Processing helix chain 'E' and resid 185 through 195 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 225 through 231 Processing helix chain 'E' and resid 232 through 241 Processing helix chain 'E' and resid 302 through 320 removed outlier: 3.831A pdb=" N ASN E 320 " --> pdb=" O TYR E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 327 Processing helix chain 'E' and resid 329 through 343 Processing helix chain 'E' and resid 348 through 358 removed outlier: 3.736A pdb=" N GLU E 352 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.962A pdb=" N ASP E 379 " --> pdb=" O VAL E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 430 through 441 Processing helix chain 'E' and resid 468 through 473 removed outlier: 3.606A pdb=" N TYR E 472 " --> pdb=" O LEU E 468 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS E 473 " --> pdb=" O ALA E 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 468 through 473' Processing helix chain 'F' and resid 16 through 21 removed outlier: 4.042A pdb=" N SER F 19 " --> pdb=" O ASP F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 44 Processing helix chain 'F' and resid 45 through 48 removed outlier: 3.647A pdb=" N LYS F 48 " --> pdb=" O GLU F 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 45 through 48' Processing helix chain 'F' and resid 79 through 94 Processing helix chain 'F' and resid 99 through 114 Processing helix chain 'F' and resid 117 through 124 Processing helix chain 'F' and resid 147 through 167 Processing helix chain 'F' and resid 185 through 195 Processing helix chain 'F' and resid 208 through 213 Processing helix chain 'F' and resid 229 through 241 removed outlier: 3.554A pdb=" N ILE F 233 " --> pdb=" O GLN F 229 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU F 234 " --> pdb=" O LYS F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 319 Processing helix chain 'F' and resid 322 through 327 Processing helix chain 'F' and resid 329 through 343 removed outlier: 3.676A pdb=" N LYS F 338 " --> pdb=" O GLU F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 359 removed outlier: 3.641A pdb=" N ARG F 359 " --> pdb=" O GLU F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 378 Processing helix chain 'F' and resid 412 through 419 Processing helix chain 'F' and resid 430 through 442 removed outlier: 3.521A pdb=" N LYS F 434 " --> pdb=" O HIS F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 472 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 62 removed outlier: 3.787A pdb=" N VAL A 59 " --> pdb=" O ASP A 54 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N PHE A 116 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR A 53 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 223 removed outlier: 5.750A pdb=" N CYS A 220 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N THR A 267 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A 222 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE A 176 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR A 268 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU A 178 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 245 Processing sheet with id=AA4, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AA5, first strand: chain 'A' and resid 450 through 453 Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 54 removed outlier: 3.669A pdb=" N VAL B 59 " --> pdb=" O ASP B 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 198 through 199 removed outlier: 6.529A pdb=" N ASN B 199 " --> pdb=" O GLU B 221 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU B 223 " --> pdb=" O ASN B 199 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N CYS B 220 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR B 267 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 222 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 176 " --> pdb=" O PHE B 264 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N MET B 175 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE B 286 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE B 177 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 244 through 247 Processing sheet with id=AA9, first strand: chain 'B' and resid 361 through 362 Processing sheet with id=AB1, first strand: chain 'B' and resid 410 through 411 Processing sheet with id=AB2, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.860A pdb=" N VAL C 59 " --> pdb=" O ASP C 54 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 198 through 199 removed outlier: 6.654A pdb=" N ASN C 199 " --> pdb=" O GLU C 221 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLU C 223 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 267 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE C 176 " --> pdb=" O PHE C 264 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N MET C 175 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE C 286 " --> pdb=" O MET C 175 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE C 177 " --> pdb=" O ILE C 286 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 244 through 248 Processing sheet with id=AB5, first strand: chain 'C' and resid 361 through 362 Processing sheet with id=AB6, first strand: chain 'C' and resid 410 through 411 Processing sheet with id=AB7, first strand: chain 'D' and resid 59 through 62 removed outlier: 3.548A pdb=" N VAL D 59 " --> pdb=" O ASP D 54 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N PHE D 116 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR D 53 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 198 through 199 removed outlier: 6.484A pdb=" N ASN D 199 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N CYS D 220 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR D 267 " --> pdb=" O CYS D 220 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE D 222 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE D 176 " --> pdb=" O PHE D 264 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N MET D 175 " --> pdb=" O PHE D 284 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE D 286 " --> pdb=" O MET D 175 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE D 177 " --> pdb=" O ILE D 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 244 through 247 Processing sheet with id=AC1, first strand: chain 'D' and resid 361 through 362 Processing sheet with id=AC2, first strand: chain 'D' and resid 385 through 386 removed outlier: 3.504A pdb=" N TYR D 385 " --> pdb=" O LEU D 397 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 450 through 453 Processing sheet with id=AC4, first strand: chain 'E' and resid 23 through 24 removed outlier: 3.690A pdb=" N ALA E 29 " --> pdb=" O SER E 24 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 59 through 62 removed outlier: 3.682A pdb=" N VAL E 59 " --> pdb=" O ASP E 54 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N PHE E 116 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N TYR E 53 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 198 through 199 removed outlier: 6.792A pdb=" N ASN E 199 " --> pdb=" O GLU E 221 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N CYS E 220 " --> pdb=" O VAL E 265 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR E 267 " --> pdb=" O CYS E 220 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE E 222 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE E 176 " --> pdb=" O PHE E 264 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N MET E 175 " --> pdb=" O PHE E 284 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE E 286 " --> pdb=" O MET E 175 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE E 177 " --> pdb=" O ILE E 286 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR E 288 " --> pdb=" O ILE E 177 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR E 179 " --> pdb=" O THR E 288 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 244 through 248 Processing sheet with id=AC8, first strand: chain 'E' and resid 361 through 362 Processing sheet with id=AC9, first strand: chain 'E' and resid 410 through 411 removed outlier: 4.661A pdb=" N SER E 465 " --> pdb=" O VAL E 448 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL E 448 " --> pdb=" O SER E 465 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 59 through 61 removed outlier: 6.060A pdb=" N TYR F 53 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 198 through 199 removed outlier: 6.598A pdb=" N ASN F 199 " --> pdb=" O GLU F 221 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLU F 223 " --> pdb=" O ASN F 199 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE F 176 " --> pdb=" O GLY F 266 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N THR F 268 " --> pdb=" O ILE F 176 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU F 178 " --> pdb=" O THR F 268 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 361 through 362 Processing sheet with id=AD4, first strand: chain 'F' and resid 386 through 387 Processing sheet with id=AD5, first strand: chain 'F' and resid 410 through 411 877 hydrogen bonds defined for protein. 2472 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.97 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7304 1.36 - 1.51: 6656 1.51 - 1.65: 8957 1.65 - 1.80: 123 1.80 - 1.95: 21 Bond restraints: 23061 Sorted by residual: bond pdb=" N ILE B 243 " pdb=" CA ILE B 243 " ideal model delta sigma weight residual 1.452 1.494 -0.042 1.18e-02 7.18e+03 1.27e+01 bond pdb=" N VAL D 244 " pdb=" CA VAL D 244 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N VAL D 51 " pdb=" CA VAL D 51 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.18e-02 7.18e+03 1.04e+01 bond pdb=" N VAL B 96 " pdb=" CA VAL B 96 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N ASP C 129 " pdb=" CA ASP C 129 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.17e-02 7.31e+03 9.98e+00 ... (remaining 23056 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 30893 2.85 - 5.70: 233 5.70 - 8.55: 21 8.55 - 11.40: 1 11.40 - 14.25: 4 Bond angle restraints: 31152 Sorted by residual: angle pdb=" N LYS C 292 " pdb=" CA LYS C 292 " pdb=" C LYS C 292 " ideal model delta sigma weight residual 113.38 106.47 6.91 1.23e+00 6.61e-01 3.16e+01 angle pdb=" CA ILE C 222 " pdb=" C ILE C 222 " pdb=" O ILE C 222 " ideal model delta sigma weight residual 122.63 118.15 4.48 8.70e-01 1.32e+00 2.65e+01 angle pdb=" PA AGS C 501 " pdb=" O3A AGS C 501 " pdb=" PB AGS C 501 " ideal model delta sigma weight residual 119.76 134.01 -14.25 3.00e+00 1.11e-01 2.26e+01 angle pdb=" PA AGS A 501 " pdb=" O3A AGS A 501 " pdb=" PB AGS A 501 " ideal model delta sigma weight residual 119.76 133.36 -13.60 3.00e+00 1.11e-01 2.06e+01 angle pdb=" PB AGS A 501 " pdb=" O3B AGS A 501 " pdb=" PG AGS A 501 " ideal model delta sigma weight residual 120.12 133.40 -13.28 3.00e+00 1.11e-01 1.96e+01 ... (remaining 31147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.69: 13210 28.69 - 57.38: 527 57.38 - 86.07: 48 86.07 - 114.77: 2 114.77 - 143.46: 4 Dihedral angle restraints: 13791 sinusoidal: 5819 harmonic: 7972 Sorted by residual: dihedral pdb=" O1A AGS A 501 " pdb=" O3A AGS A 501 " pdb=" PA AGS A 501 " pdb=" PB AGS A 501 " ideal model delta sinusoidal sigma weight residual -67.73 75.73 -143.46 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" O1A AGS C 501 " pdb=" O3A AGS C 501 " pdb=" PA AGS C 501 " pdb=" PB AGS C 501 " ideal model delta sinusoidal sigma weight residual -67.73 61.20 -128.93 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" O1B AGS C 501 " pdb=" O3B AGS C 501 " pdb=" PB AGS C 501 " pdb=" PG AGS C 501 " ideal model delta sinusoidal sigma weight residual 68.91 -57.96 126.87 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 13788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2805 0.063 - 0.126: 442 0.126 - 0.189: 47 0.189 - 0.252: 9 0.252 - 0.316: 3 Chirality restraints: 3306 Sorted by residual: chirality pdb=" CA ILE A 222 " pdb=" N ILE A 222 " pdb=" C ILE A 222 " pdb=" CB ILE A 222 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA LEU E 214 " pdb=" N LEU E 214 " pdb=" C LEU E 214 " pdb=" CB LEU E 214 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA HIS B 378 " pdb=" N HIS B 378 " pdb=" C HIS B 378 " pdb=" CB HIS B 378 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 3303 not shown) Planarity restraints: 3909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 258 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO A 259 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 94 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C TYR B 94 " -0.039 2.00e-02 2.50e+03 pdb=" O TYR B 94 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN B 95 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 167 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO B 168 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 168 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 168 " -0.029 5.00e-02 4.00e+02 ... (remaining 3906 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 92 2.43 - 3.05: 14312 3.05 - 3.67: 33600 3.67 - 4.28: 53240 4.28 - 4.90: 89026 Nonbonded interactions: 190270 Sorted by model distance: nonbonded pdb=" S1G AGS A 501 " pdb="MG MG A 502 " model vdw 1.818 2.530 nonbonded pdb=" S1G AGS C 501 " pdb="MG MG C 502 " model vdw 1.839 2.530 nonbonded pdb=" O1B AGS B 501 " pdb="MG MG B 502 " model vdw 2.072 2.170 nonbonded pdb=" O1B AGS D 501 " pdb="MG MG D 502 " model vdw 2.111 2.170 nonbonded pdb=" O3G AGS B 501 " pdb="MG MG B 502 " model vdw 2.166 2.170 ... (remaining 190265 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 15 through 248 or resid 251 through 381 or resid 386 or re \ sid 388 or (resid 401 and (name N or name CA or name C or name O or name CB )) o \ r resid 402 through 472)) selection = (chain 'B' and (resid 15 through 248 or resid 251 through 381 or resid 395 or re \ sid 397 or (resid 401 and (name N or name CA or name C or name O or name CB )) o \ r resid 402 through 472)) selection = (chain 'C' and (resid 15 through 248 or resid 251 through 381 or resid 386 throu \ gh 394 or (resid 401 and (name N or name CA or name C or name O or name CB )) or \ resid 402 through 472)) selection = (chain 'D' and (resid 15 through 248 or resid 251 through 381 or resid 386 or re \ sid 394 or (resid 401 and (name N or name CA or name C or name O or name CB )) o \ r resid 402 through 472)) selection = (chain 'E' and (resid 15 through 248 or resid 251 through 381 or resid 386 or re \ sid 388 or resid 401 through 472)) selection = (chain 'F' and (resid 15 through 381 or resid 386 or resid 388 or (resid 401 and \ (name N or name CA or name C or name O or name CB )) or resid 402 through 472)) \ } 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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 22.220 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 23061 Z= 0.309 Angle : 0.683 14.254 31152 Z= 0.442 Chirality : 0.048 0.316 3306 Planarity : 0.003 0.057 3909 Dihedral : 14.862 143.458 8673 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.25 % Allowed : 0.79 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.15), residues: 2681 helix: 0.46 (0.15), residues: 1153 sheet: -1.02 (0.30), residues: 279 loop : -1.32 (0.16), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 314 TYR 0.015 0.001 TYR D 94 PHE 0.017 0.001 PHE F 116 TRP 0.016 0.001 TRP C 197 HIS 0.009 0.001 HIS F 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.31 (23061) covalent geometry : angle 0.68347 / 0.44 (31152) hydrogen bonds : bond 0.14907 / 9.83 ( 877) hydrogen bonds : angle 6.24614 / 4.45 ( 2472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 302 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7767 (tttp) cc_final: 0.7489 (ttmt) REVERT: A 292 LYS cc_start: 0.8148 (mmmm) cc_final: 0.7729 (mtpp) REVERT: A 452 THR cc_start: 0.8279 (m) cc_final: 0.7993 (p) REVERT: B 38 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7224 (mt-10) REVERT: B 291 ASN cc_start: 0.7449 (m-40) cc_final: 0.7186 (m110) REVERT: B 330 LYS cc_start: 0.7540 (tttm) cc_final: 0.7258 (tttm) REVERT: B 405 TYR cc_start: 0.8659 (m-80) cc_final: 0.8173 (m-80) REVERT: B 453 ARG cc_start: 0.8119 (ptp-110) cc_final: 0.7581 (mtm180) REVERT: C 235 ASP cc_start: 0.7425 (t0) cc_final: 0.7193 (t0) REVERT: C 436 ASP cc_start: 0.7516 (m-30) cc_final: 0.6992 (m-30) REVERT: D 99 SER cc_start: 0.8842 (m) cc_final: 0.8601 (p) REVERT: D 206 LYS cc_start: 0.8412 (ptpp) cc_final: 0.8046 (mtpt) REVERT: D 209 GLU cc_start: 0.7662 (tp30) cc_final: 0.7441 (mm-30) REVERT: D 234 GLU cc_start: 0.7519 (mp0) cc_final: 0.7057 (mp0) REVERT: D 367 TYR cc_start: 0.7934 (m-80) cc_final: 0.7575 (m-80) REVERT: E 224 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6645 (mm-30) REVERT: E 254 ARG cc_start: 0.6898 (ptp-110) cc_final: 0.6039 (ptm-80) REVERT: E 324 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8192 (tttp) REVERT: E 341 GLU cc_start: 0.7313 (tm-30) cc_final: 0.7066 (tp30) REVERT: F 341 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6673 (mm-30) REVERT: F 453 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7543 (mmm160) outliers start: 6 outliers final: 0 residues processed: 306 average time/residue: 0.1808 time to fit residues: 84.3308 Evaluate side-chains 201 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 HIS ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 431 HIS C 147 ASN C 200 GLN D 196 HIS D 200 GLN D 426 GLN E 443 ASN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.087911 restraints weight = 35330.773| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.59 r_work: 0.2886 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 23061 Z= 0.224 Angle : 0.559 6.846 31152 Z= 0.303 Chirality : 0.043 0.175 3306 Planarity : 0.004 0.050 3909 Dihedral : 9.714 160.227 3115 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.92 % Allowed : 7.13 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.15), residues: 2681 helix: 0.40 (0.15), residues: 1187 sheet: -1.31 (0.28), residues: 282 loop : -1.35 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 282 TYR 0.024 0.002 TYR A 472 PHE 0.016 0.002 PHE D 283 TRP 0.014 0.002 TRP C 128 HIS 0.009 0.001 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.22 (23061) covalent geometry : angle 0.55890 / 0.30 (31152) hydrogen bonds : bond 0.04838 / 3.21 ( 877) hydrogen bonds : angle 5.11168 / 3.66 ( 2472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8194 (tttp) cc_final: 0.7826 (ttmt) REVERT: A 292 LYS cc_start: 0.8078 (mmmm) cc_final: 0.7746 (mtpp) REVERT: B 405 TYR cc_start: 0.8715 (m-80) cc_final: 0.8077 (m-80) REVERT: B 453 ARG cc_start: 0.8419 (ptp-110) cc_final: 0.7773 (mtm180) REVERT: C 235 ASP cc_start: 0.8102 (t0) cc_final: 0.7824 (t0) REVERT: D 206 LYS cc_start: 0.8698 (ptpp) cc_final: 0.8269 (mtpt) REVERT: D 209 GLU cc_start: 0.8001 (tp30) cc_final: 0.7648 (tp30) REVERT: D 234 GLU cc_start: 0.7995 (mp0) cc_final: 0.7406 (mp0) REVERT: D 367 TYR cc_start: 0.8397 (m-80) cc_final: 0.7992 (m-80) REVERT: E 224 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7069 (mm-30) REVERT: E 226 SER cc_start: 0.7974 (p) cc_final: 0.7734 (m) REVERT: E 254 ARG cc_start: 0.6954 (ptp-110) cc_final: 0.5999 (ptm-80) REVERT: E 324 LYS cc_start: 0.8509 (ttpt) cc_final: 0.8134 (tttp) REVERT: E 341 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7175 (tp30) REVERT: F 237 LYS cc_start: 0.6969 (mtmt) cc_final: 0.6500 (mtmt) REVERT: F 318 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: F 341 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7048 (mm-30) outliers start: 22 outliers final: 15 residues processed: 206 average time/residue: 0.1707 time to fit residues: 54.8710 Evaluate side-chains 192 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain F residue 318 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 12 optimal weight: 0.9980 chunk 264 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 244 optimal weight: 0.3980 chunk 189 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 291 ASN C 114 ASN D 196 HIS ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.094224 restraints weight = 34552.618| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.31 r_work: 0.2924 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23061 Z= 0.174 Angle : 0.494 6.809 31152 Z= 0.269 Chirality : 0.041 0.172 3306 Planarity : 0.004 0.049 3909 Dihedral : 9.586 157.357 3115 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.38 % Allowed : 8.92 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.15), residues: 2681 helix: 0.54 (0.15), residues: 1185 sheet: -1.31 (0.27), residues: 292 loop : -1.31 (0.16), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 260 TYR 0.020 0.001 TYR A 472 PHE 0.013 0.001 PHE D 283 TRP 0.013 0.001 TRP C 197 HIS 0.010 0.001 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (23061) covalent geometry : angle 0.49421 / 0.27 (31152) hydrogen bonds : bond 0.04556 / 3.02 ( 877) hydrogen bonds : angle 4.90379 / 3.51 ( 2472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8226 (tttp) cc_final: 0.7928 (ttmt) REVERT: A 292 LYS cc_start: 0.8292 (mmmm) cc_final: 0.7991 (mtpp) REVERT: B 453 ARG cc_start: 0.8412 (ptp-110) cc_final: 0.7765 (mtp85) REVERT: C 235 ASP cc_start: 0.8051 (t0) cc_final: 0.7787 (t0) REVERT: D 209 GLU cc_start: 0.8036 (tp30) cc_final: 0.7698 (tp30) REVERT: D 234 GLU cc_start: 0.7893 (mp0) cc_final: 0.7392 (mp0) REVERT: D 367 TYR cc_start: 0.8313 (m-80) cc_final: 0.7940 (m-80) REVERT: D 466 VAL cc_start: 0.9260 (OUTLIER) cc_final: 0.9010 (t) REVERT: E 224 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6982 (mm-30) REVERT: E 226 SER cc_start: 0.8097 (p) cc_final: 0.7871 (m) REVERT: E 254 ARG cc_start: 0.6930 (ptp-110) cc_final: 0.6110 (ptt180) REVERT: E 324 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8349 (tttp) REVERT: E 341 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7319 (tp30) REVERT: E 443 ASN cc_start: 0.8021 (t160) cc_final: 0.7772 (t0) REVERT: F 341 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7083 (mm-30) outliers start: 33 outliers final: 21 residues processed: 219 average time/residue: 0.1518 time to fit residues: 52.4269 Evaluate side-chains 201 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 381 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 176 optimal weight: 0.0010 chunk 115 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 227 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 189 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 291 ASN C 117 HIS D 196 HIS E 443 ASN F 426 GLN F 428 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.111347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.094371 restraints weight = 34619.400| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.37 r_work: 0.2954 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23061 Z= 0.102 Angle : 0.438 6.749 31152 Z= 0.239 Chirality : 0.039 0.161 3306 Planarity : 0.003 0.048 3909 Dihedral : 9.375 155.522 3115 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.25 % Allowed : 10.50 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.16), residues: 2681 helix: 0.80 (0.15), residues: 1192 sheet: -1.44 (0.27), residues: 294 loop : -1.26 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 314 TYR 0.017 0.001 TYR F 198 PHE 0.012 0.001 PHE F 56 TRP 0.011 0.001 TRP F 197 HIS 0.012 0.001 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (23061) covalent geometry : angle 0.43834 / 0.24 (31152) hydrogen bonds : bond 0.03781 / 2.47 ( 877) hydrogen bonds : angle 4.66936 / 3.34 ( 2472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8183 (tttp) cc_final: 0.7847 (ttmt) REVERT: A 292 LYS cc_start: 0.8240 (mmmm) cc_final: 0.7944 (mtpp) REVERT: B 453 ARG cc_start: 0.8390 (ptp-110) cc_final: 0.7859 (mtp85) REVERT: C 235 ASP cc_start: 0.8049 (t0) cc_final: 0.7791 (t0) REVERT: D 209 GLU cc_start: 0.7995 (tp30) cc_final: 0.7508 (mm-30) REVERT: D 234 GLU cc_start: 0.7952 (mp0) cc_final: 0.7603 (mp0) REVERT: D 367 TYR cc_start: 0.8317 (m-80) cc_final: 0.7955 (m-80) REVERT: D 466 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.9014 (t) REVERT: E 165 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8208 (tp) REVERT: E 224 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7008 (mm-30) REVERT: E 226 SER cc_start: 0.8008 (p) cc_final: 0.7763 (m) REVERT: E 254 ARG cc_start: 0.6849 (ptp-110) cc_final: 0.6092 (ptt180) REVERT: E 324 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8227 (ttmm) REVERT: E 341 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7358 (tp30) REVERT: E 443 ASN cc_start: 0.8032 (t0) cc_final: 0.7824 (t0) REVERT: F 335 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5437 (tmm) REVERT: F 341 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7045 (mm-30) outliers start: 30 outliers final: 15 residues processed: 214 average time/residue: 0.1612 time to fit residues: 53.8582 Evaluate side-chains 196 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain D residue 42 CYS Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain F residue 335 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 249 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 256 optimal weight: 6.9990 chunk 262 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 215 optimal weight: 0.0060 chunk 63 optimal weight: 1.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 ASN D 196 HIS D 200 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.089017 restraints weight = 34462.966| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.77 r_work: 0.2924 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23061 Z= 0.120 Angle : 0.440 6.666 31152 Z= 0.239 Chirality : 0.039 0.167 3306 Planarity : 0.003 0.048 3909 Dihedral : 9.241 155.665 3115 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.58 % Allowed : 10.88 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.16), residues: 2681 helix: 0.93 (0.15), residues: 1181 sheet: -1.27 (0.27), residues: 295 loop : -1.18 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 314 TYR 0.017 0.001 TYR A 472 PHE 0.009 0.001 PHE C 310 TRP 0.010 0.001 TRP C 197 HIS 0.011 0.001 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (23061) covalent geometry : angle 0.43978 / 0.24 (31152) hydrogen bonds : bond 0.03803 / 2.50 ( 877) hydrogen bonds : angle 4.59058 / 3.29 ( 2472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.901 Fit side-chains REVERT: A 92 LYS cc_start: 0.8250 (tttp) cc_final: 0.7850 (ttmt) REVERT: A 292 LYS cc_start: 0.8201 (mmmm) cc_final: 0.7912 (mtpp) REVERT: B 453 ARG cc_start: 0.8483 (ptp-110) cc_final: 0.7846 (mtp85) REVERT: C 235 ASP cc_start: 0.8159 (t0) cc_final: 0.7889 (t0) REVERT: C 436 ASP cc_start: 0.8375 (m-30) cc_final: 0.7829 (m-30) REVERT: D 209 GLU cc_start: 0.8072 (tp30) cc_final: 0.7552 (mm-30) REVERT: D 214 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8551 (mp) REVERT: D 234 GLU cc_start: 0.8091 (mp0) cc_final: 0.7665 (mp0) REVERT: D 367 TYR cc_start: 0.8473 (m-80) cc_final: 0.8119 (m-80) REVERT: D 466 VAL cc_start: 0.9251 (OUTLIER) cc_final: 0.8971 (t) REVERT: E 140 ASP cc_start: 0.8121 (p0) cc_final: 0.7917 (p0) REVERT: E 165 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8205 (tp) REVERT: E 224 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7166 (mm-30) REVERT: E 226 SER cc_start: 0.8035 (p) cc_final: 0.7804 (m) REVERT: E 254 ARG cc_start: 0.6895 (ptp-110) cc_final: 0.6049 (ptt180) REVERT: E 324 LYS cc_start: 0.8543 (ttpt) cc_final: 0.8135 (ttmm) REVERT: E 443 ASN cc_start: 0.8145 (t0) cc_final: 0.7928 (t0) REVERT: F 247 TYR cc_start: 0.5667 (t80) cc_final: 0.5447 (t80) REVERT: F 335 MET cc_start: 0.6112 (OUTLIER) cc_final: 0.5087 (tmm) REVERT: F 341 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7100 (mm-30) outliers start: 38 outliers final: 22 residues processed: 214 average time/residue: 0.1576 time to fit residues: 52.9660 Evaluate side-chains 203 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 406 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 68 optimal weight: 8.9990 chunk 259 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 267 optimal weight: 0.9990 chunk 123 optimal weight: 0.0770 chunk 206 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 GLN ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 ASN C 147 ASN D 196 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095635 restraints weight = 34015.211| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.38 r_work: 0.2950 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23061 Z= 0.119 Angle : 0.439 6.427 31152 Z= 0.238 Chirality : 0.039 0.166 3306 Planarity : 0.003 0.049 3909 Dihedral : 9.143 155.259 3115 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.88 % Allowed : 11.13 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.16), residues: 2681 helix: 1.02 (0.15), residues: 1175 sheet: -1.26 (0.27), residues: 295 loop : -1.10 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 314 TYR 0.024 0.001 TYR F 316 PHE 0.009 0.001 PHE C 310 TRP 0.009 0.001 TRP F 417 HIS 0.011 0.001 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (23061) covalent geometry : angle 0.43854 / 0.24 (31152) hydrogen bonds : bond 0.03749 / 2.46 ( 877) hydrogen bonds : angle 4.53505 / 3.25 ( 2472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.894 Fit side-chains REVERT: A 92 LYS cc_start: 0.8138 (tttp) cc_final: 0.7717 (ttmt) REVERT: A 292 LYS cc_start: 0.8156 (mmmm) cc_final: 0.7888 (mtpp) REVERT: B 453 ARG cc_start: 0.8364 (ptp-110) cc_final: 0.7826 (mtp85) REVERT: C 235 ASP cc_start: 0.7974 (t0) cc_final: 0.7706 (t0) REVERT: C 436 ASP cc_start: 0.8205 (m-30) cc_final: 0.7687 (m-30) REVERT: D 209 GLU cc_start: 0.7943 (tp30) cc_final: 0.7407 (mm-30) REVERT: D 214 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8464 (mp) REVERT: D 234 GLU cc_start: 0.7925 (mp0) cc_final: 0.7470 (mp0) REVERT: D 367 TYR cc_start: 0.8343 (m-80) cc_final: 0.7980 (m-80) REVERT: D 466 VAL cc_start: 0.9185 (OUTLIER) cc_final: 0.8938 (t) REVERT: E 140 ASP cc_start: 0.8014 (p0) cc_final: 0.7800 (p0) REVERT: E 165 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8229 (tp) REVERT: E 224 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7081 (mm-30) REVERT: E 226 SER cc_start: 0.7947 (p) cc_final: 0.7715 (m) REVERT: E 254 ARG cc_start: 0.6747 (ptp-110) cc_final: 0.5971 (ptt180) REVERT: E 324 LYS cc_start: 0.8417 (ttpt) cc_final: 0.7999 (ttmm) REVERT: E 443 ASN cc_start: 0.8021 (t0) cc_final: 0.7814 (t0) REVERT: F 247 TYR cc_start: 0.5684 (t80) cc_final: 0.5398 (t80) REVERT: F 335 MET cc_start: 0.5988 (OUTLIER) cc_final: 0.4870 (tmm) REVERT: F 341 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7092 (mm-30) outliers start: 45 outliers final: 28 residues processed: 218 average time/residue: 0.1589 time to fit residues: 54.6110 Evaluate side-chains 208 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 406 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 196 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 267 optimal weight: 8.9990 chunk 174 optimal weight: 0.7980 chunk 265 optimal weight: 5.9990 chunk 119 optimal weight: 0.0770 chunk 136 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 254 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 ASN D 196 HIS D 200 GLN E 89 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093939 restraints weight = 34314.711| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.41 r_work: 0.2964 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23061 Z= 0.094 Angle : 0.418 6.217 31152 Z= 0.227 Chirality : 0.038 0.161 3306 Planarity : 0.003 0.053 3909 Dihedral : 8.953 154.633 3115 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.38 % Allowed : 11.92 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.16), residues: 2681 helix: 1.12 (0.15), residues: 1181 sheet: -1.29 (0.27), residues: 291 loop : -1.08 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 314 TYR 0.015 0.001 TYR B 472 PHE 0.008 0.001 PHE F 56 TRP 0.009 0.001 TRP C 197 HIS 0.011 0.001 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 (23061) covalent geometry : angle 0.41845 / 0.23 (31152) hydrogen bonds : bond 0.03459 / 2.25 ( 877) hydrogen bonds : angle 4.42516 / 3.17 ( 2472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.949 Fit side-chains REVERT: A 92 LYS cc_start: 0.8114 (tttp) cc_final: 0.7695 (ttmt) REVERT: A 110 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: A 292 LYS cc_start: 0.8164 (mmmm) cc_final: 0.7911 (mtpp) REVERT: B 453 ARG cc_start: 0.8343 (ptp-110) cc_final: 0.7837 (mtp85) REVERT: C 235 ASP cc_start: 0.7978 (t0) cc_final: 0.7612 (t70) REVERT: C 436 ASP cc_start: 0.8214 (m-30) cc_final: 0.7733 (m-30) REVERT: D 209 GLU cc_start: 0.7939 (tp30) cc_final: 0.7418 (mm-30) REVERT: D 234 GLU cc_start: 0.7955 (mp0) cc_final: 0.7496 (mp0) REVERT: D 367 TYR cc_start: 0.8342 (m-80) cc_final: 0.7984 (m-80) REVERT: D 466 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8936 (t) REVERT: E 140 ASP cc_start: 0.7996 (p0) cc_final: 0.7748 (p0) REVERT: E 165 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8217 (tp) REVERT: E 226 SER cc_start: 0.7935 (p) cc_final: 0.7717 (m) REVERT: E 254 ARG cc_start: 0.6701 (ptp-110) cc_final: 0.5959 (ptt180) REVERT: E 324 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8036 (ttmm) REVERT: E 409 ASP cc_start: 0.7814 (t70) cc_final: 0.7562 (t70) REVERT: E 415 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: E 443 ASN cc_start: 0.7948 (t0) cc_final: 0.7623 (t0) REVERT: F 247 TYR cc_start: 0.5745 (t80) cc_final: 0.5447 (t80) REVERT: F 335 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.4918 (tmm) REVERT: F 341 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7043 (mm-30) outliers start: 33 outliers final: 20 residues processed: 218 average time/residue: 0.1639 time to fit residues: 55.6106 Evaluate side-chains 203 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 380 VAL Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 406 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 216 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 chunk 224 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 268 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 ASN D 196 HIS F 196 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.109215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.092101 restraints weight = 34286.206| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.37 r_work: 0.2919 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23061 Z= 0.189 Angle : 0.486 6.311 31152 Z= 0.262 Chirality : 0.041 0.173 3306 Planarity : 0.004 0.050 3909 Dihedral : 8.983 154.712 3115 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.75 % Allowed : 11.92 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.16), residues: 2681 helix: 0.92 (0.15), residues: 1180 sheet: -1.24 (0.27), residues: 285 loop : -1.14 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 314 TYR 0.020 0.001 TYR F 198 PHE 0.012 0.001 PHE D 283 TRP 0.012 0.001 TRP F 417 HIS 0.011 0.001 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (23061) covalent geometry : angle 0.48609 / 0.26 (31152) hydrogen bonds : bond 0.04126 / 2.74 ( 877) hydrogen bonds : angle 4.59952 / 3.30 ( 2472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.967 Fit side-chains REVERT: A 92 LYS cc_start: 0.8189 (tttp) cc_final: 0.7770 (ttmt) REVERT: A 110 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: A 292 LYS cc_start: 0.8172 (mmmm) cc_final: 0.7933 (mtpp) REVERT: B 453 ARG cc_start: 0.8363 (ptp-110) cc_final: 0.7698 (mtp85) REVERT: C 235 ASP cc_start: 0.7992 (t0) cc_final: 0.7714 (t0) REVERT: C 436 ASP cc_start: 0.8232 (m-30) cc_final: 0.7693 (m-30) REVERT: D 209 GLU cc_start: 0.7995 (tp30) cc_final: 0.7436 (mm-30) REVERT: D 214 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8482 (mp) REVERT: D 234 GLU cc_start: 0.7924 (mp0) cc_final: 0.7467 (mp0) REVERT: D 367 TYR cc_start: 0.8361 (m-80) cc_final: 0.8016 (m-80) REVERT: D 466 VAL cc_start: 0.9193 (OUTLIER) cc_final: 0.8911 (t) REVERT: E 165 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8203 (tp) REVERT: E 214 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7987 (mp) REVERT: E 224 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7114 (mm-30) REVERT: E 226 SER cc_start: 0.8004 (p) cc_final: 0.7748 (m) REVERT: E 254 ARG cc_start: 0.6676 (ptp-110) cc_final: 0.5941 (ptt180) REVERT: E 324 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8038 (ttmm) REVERT: E 415 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: E 443 ASN cc_start: 0.7963 (t0) cc_final: 0.7622 (t0) REVERT: F 335 MET cc_start: 0.6084 (OUTLIER) cc_final: 0.5049 (tmm) REVERT: F 341 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7100 (mm-30) outliers start: 42 outliers final: 29 residues processed: 210 average time/residue: 0.1601 time to fit residues: 52.6991 Evaluate side-chains 209 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 406 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 81 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 234 optimal weight: 0.3980 chunk 211 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 HIS B 291 ASN D 196 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.092819 restraints weight = 34253.227| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.41 r_work: 0.2915 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23061 Z= 0.175 Angle : 0.482 6.303 31152 Z= 0.260 Chirality : 0.041 0.173 3306 Planarity : 0.004 0.049 3909 Dihedral : 8.980 155.044 3115 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.83 % Allowed : 12.01 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.16), residues: 2681 helix: 0.86 (0.15), residues: 1180 sheet: -1.28 (0.27), residues: 293 loop : -1.14 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 314 TYR 0.019 0.001 TYR A 472 PHE 0.011 0.001 PHE D 283 TRP 0.011 0.001 TRP F 417 HIS 0.011 0.001 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (23061) covalent geometry : angle 0.48216 / 0.26 (31152) hydrogen bonds : bond 0.04101 / 2.71 ( 877) hydrogen bonds : angle 4.60322 / 3.30 ( 2472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 0.851 Fit side-chains REVERT: A 92 LYS cc_start: 0.8177 (tttp) cc_final: 0.7743 (ttmt) REVERT: A 110 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7671 (tm-30) REVERT: A 292 LYS cc_start: 0.8154 (mmmm) cc_final: 0.7913 (mtpp) REVERT: B 453 ARG cc_start: 0.8362 (ptp-110) cc_final: 0.7675 (mtp85) REVERT: C 235 ASP cc_start: 0.8001 (t0) cc_final: 0.7711 (t0) REVERT: C 436 ASP cc_start: 0.8248 (m-30) cc_final: 0.7697 (m-30) REVERT: D 209 GLU cc_start: 0.8009 (tp30) cc_final: 0.7408 (mm-30) REVERT: D 214 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8515 (mp) REVERT: D 234 GLU cc_start: 0.7922 (mp0) cc_final: 0.7462 (mp0) REVERT: D 367 TYR cc_start: 0.8359 (m-80) cc_final: 0.8011 (m-80) REVERT: D 466 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8893 (t) REVERT: E 165 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8211 (tp) REVERT: E 214 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7994 (mp) REVERT: E 224 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7121 (mm-30) REVERT: E 226 SER cc_start: 0.8038 (p) cc_final: 0.7743 (m) REVERT: E 254 ARG cc_start: 0.6658 (ptp-110) cc_final: 0.5815 (ptt180) REVERT: E 324 LYS cc_start: 0.8426 (ttpt) cc_final: 0.7951 (ttmm) REVERT: E 415 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: E 443 ASN cc_start: 0.8065 (t0) cc_final: 0.7680 (t0) REVERT: F 335 MET cc_start: 0.6112 (OUTLIER) cc_final: 0.5155 (tmm) REVERT: F 341 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7147 (mm-30) outliers start: 44 outliers final: 29 residues processed: 205 average time/residue: 0.1637 time to fit residues: 52.4614 Evaluate side-chains 207 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 406 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 57 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 257 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 196 HIS D 308 GLN E 117 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094760 restraints weight = 34179.682| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.42 r_work: 0.2952 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23061 Z= 0.107 Angle : 0.438 6.055 31152 Z= 0.237 Chirality : 0.039 0.166 3306 Planarity : 0.003 0.051 3909 Dihedral : 8.847 154.808 3115 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.46 % Allowed : 12.34 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.16), residues: 2681 helix: 1.10 (0.15), residues: 1174 sheet: -1.29 (0.27), residues: 293 loop : -1.05 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 314 TYR 0.018 0.001 TYR F 198 PHE 0.008 0.001 PHE F 56 TRP 0.010 0.001 TRP C 366 HIS 0.012 0.001 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (23061) covalent geometry : angle 0.43800 / 0.24 (31152) hydrogen bonds : bond 0.03645 / 2.38 ( 877) hydrogen bonds : angle 4.48127 / 3.22 ( 2472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.933 Fit side-chains REVERT: A 92 LYS cc_start: 0.8167 (tttp) cc_final: 0.7731 (ttmt) REVERT: A 110 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: A 292 LYS cc_start: 0.8131 (mmmm) cc_final: 0.7894 (mtpp) REVERT: B 453 ARG cc_start: 0.8318 (ptp-110) cc_final: 0.7756 (mtp85) REVERT: C 235 ASP cc_start: 0.7973 (t0) cc_final: 0.7694 (t0) REVERT: C 436 ASP cc_start: 0.8227 (m-30) cc_final: 0.7682 (m-30) REVERT: D 209 GLU cc_start: 0.7964 (tp30) cc_final: 0.7397 (mm-30) REVERT: D 214 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8482 (mp) REVERT: D 234 GLU cc_start: 0.7927 (mp0) cc_final: 0.7476 (mp0) REVERT: D 367 TYR cc_start: 0.8342 (m-80) cc_final: 0.8003 (m-80) REVERT: D 466 VAL cc_start: 0.9129 (OUTLIER) cc_final: 0.8897 (t) REVERT: E 165 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8232 (tp) REVERT: E 214 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7996 (mp) REVERT: E 224 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7080 (mm-30) REVERT: E 254 ARG cc_start: 0.6700 (ptp-110) cc_final: 0.5843 (ptt180) REVERT: E 409 ASP cc_start: 0.7854 (t70) cc_final: 0.7621 (t70) REVERT: E 415 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: E 443 ASN cc_start: 0.7949 (t0) cc_final: 0.7575 (t0) REVERT: F 247 TYR cc_start: 0.5716 (t80) cc_final: 0.5414 (t80) REVERT: F 335 MET cc_start: 0.6001 (OUTLIER) cc_final: 0.4985 (tmm) REVERT: F 341 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7161 (mm-30) outliers start: 35 outliers final: 25 residues processed: 207 average time/residue: 0.1661 time to fit residues: 53.7614 Evaluate side-chains 207 residues out of total 2400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 406 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 165 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 42 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 62.2087 > 50:) chunk 156 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 260 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.111231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.093916 restraints weight = 34012.257| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.40 r_work: 0.2921 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23061 Z= 0.174 Angle : 0.479 5.977 31152 Z= 0.258 Chirality : 0.041 0.171 3306 Planarity : 0.004 0.049 3909 Dihedral : 8.881 154.710 3115 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.71 % Allowed : 12.38 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.16), residues: 2681 helix: 0.92 (0.15), residues: 1180 sheet: -1.28 (0.27), residues: 293 loop : -1.12 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 314 TYR 0.018 0.001 TYR A 472 PHE 0.011 0.001 PHE D 283 TRP 0.011 0.001 TRP F 417 HIS 0.010 0.001 HIS D 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (23061) covalent geometry : angle 0.47872 / 0.26 (31152) hydrogen bonds : bond 0.04037 / 2.67 ( 877) hydrogen bonds : angle 4.57900 / 3.29 ( 2472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5067.16 seconds wall clock time: 88 minutes 23.23 seconds (5303.23 seconds total)