Starting phenix.real_space_refine on Mon Oct 26 07:00:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n9w_0381/10_2026/6n9w_0381_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n9w_0381/10_2026/6n9w_0381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n9w_0381/10_2026/6n9w_0381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n9w_0381/10_2026/6n9w_0381.map" model { file = "/net/cci-nas-00/data/ceres_data/6n9w_0381/10_2026/6n9w_0381_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n9w_0381/10_2026/6n9w_0381_neut.cif" } resolution = 4.0 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= -0.002 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 44 5.49 5 Mg 6 5.21 5 S 112 5.16 5 C 12188 2.51 5 N 3418 2.21 5 O 3807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19576 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3856 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 485} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3678 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 9, 'TRANS': 464} Chain breaks: 3 Chain: "C" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2127 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 4, 'TRANS': 271} Chain breaks: 3 Chain: "D" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2016 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 256} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1861 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 236} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 134 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "H" Number of atoms: 5144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5144 Classifications: {'peptide': 645} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 622} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "P" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Unusual residues: {'DOC': 1} Classifications: {'RNA': 5, 'undetermined': 1} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna3p': 4, None: 1} Not linked: pdbres=" G P 5 " pdbres="DOC P 6 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 486 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69 SG CYS A 17 37.587 59.298 40.884 1.00181.79 S ATOM 91 SG CYS A 20 39.316 61.484 38.973 1.00181.96 S ATOM 204 SG CYS A 36 40.487 61.058 41.926 1.00161.54 S ATOM 229 SG CYS A 39 37.651 62.302 42.568 1.00174.44 S Time building chain proxies: 3.85, per 1000 atoms: 0.20 Number of scatterers: 19576 At special positions: 0 Unit cell: (111.8, 135.88, 182.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 112 16.00 P 44 15.00 Mg 6 11.99 O 3807 8.00 N 3418 7.00 C 12188 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 235 " - pdb=" SG CYS B 241 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 840.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 36 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 17 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 20 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 39 " Number of angles added : 6 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4352 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 18 sheets defined 39.2% alpha, 13.0% beta 5 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 87 through 95 removed outlier: 3.598A pdb=" N CYS A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 104 Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 184 through 192 removed outlier: 3.510A pdb=" N THR A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.647A pdb=" N GLN A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.649A pdb=" N CYS A 241 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 removed outlier: 3.749A pdb=" N GLN A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 272 through 280 removed outlier: 4.101A pdb=" N ARG A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.582A pdb=" N LEU A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 334 removed outlier: 3.525A pdb=" N PHE A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET A 333 " --> pdb=" O TRP A 329 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 334 " --> pdb=" O GLY A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 361 through 364 removed outlier: 3.810A pdb=" N GLN A 364 " --> pdb=" O ARG A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 364' Processing helix chain 'A' and resid 365 through 372 removed outlier: 3.514A pdb=" N LYS A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.523A pdb=" N TRP A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 415 removed outlier: 3.821A pdb=" N ALA A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 454 Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.624A pdb=" N GLY A 478 " --> pdb=" O HIS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.831A pdb=" N ASP A 485 " --> pdb=" O SER A 482 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU A 486 " --> pdb=" O ILE A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 486' Processing helix chain 'A' and resid 491 through 496 removed outlier: 3.591A pdb=" N SER A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 95 removed outlier: 3.899A pdb=" N CYS B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 168 removed outlier: 3.519A pdb=" N LEU B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 191 removed outlier: 3.549A pdb=" N THR B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.887A pdb=" N GLN B 198 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 199 " --> pdb=" O PHE B 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 195 through 199' Processing helix chain 'B' and resid 209 through 219 Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.884A pdb=" N CYS B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.754A pdb=" N GLU B 252 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 280 removed outlier: 3.661A pdb=" N ARG B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 334 removed outlier: 3.779A pdb=" N ALA B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 333 " --> pdb=" O TRP B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.709A pdb=" N THR B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 375 removed outlier: 3.750A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 386 removed outlier: 3.795A pdb=" N GLU B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 415 removed outlier: 3.604A pdb=" N ALA B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 430 removed outlier: 4.437A pdb=" N VAL B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 454 removed outlier: 3.647A pdb=" N MET B 441 " --> pdb=" O ASP B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.836A pdb=" N GLY B 478 " --> pdb=" O HIS B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 removed outlier: 3.657A pdb=" N ASP B 485 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B 486 " --> pdb=" O ILE B 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 482 through 486' Processing helix chain 'B' and resid 491 through 496 removed outlier: 3.749A pdb=" N LEU B 495 " --> pdb=" O ALA B 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 279 removed outlier: 3.650A pdb=" N LEU C 279 " --> pdb=" O ILE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 300 Processing helix chain 'C' and resid 317 through 332 removed outlier: 3.634A pdb=" N PHE C 321 " --> pdb=" O GLY C 317 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.782A pdb=" N ALA C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 358 removed outlier: 3.671A pdb=" N GLY C 355 " --> pdb=" O GLU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 375 removed outlier: 3.964A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 386 removed outlier: 4.006A pdb=" N GLN C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU C 385 " --> pdb=" O TRP C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 415 removed outlier: 4.250A pdb=" N LEU C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.590A pdb=" N ILE C 428 " --> pdb=" O HIS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 457 removed outlier: 4.020A pdb=" N MET C 441 " --> pdb=" O ASP C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 4.153A pdb=" N LEU C 486 " --> pdb=" O ILE C 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 279 removed outlier: 3.552A pdb=" N LEU D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 299 Processing helix chain 'D' and resid 317 through 331 removed outlier: 3.534A pdb=" N GLN D 325 " --> pdb=" O PHE D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 removed outlier: 4.016A pdb=" N THR D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 376 removed outlier: 3.987A pdb=" N GLY D 376 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 386 removed outlier: 3.646A pdb=" N GLU D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 416 Processing helix chain 'D' and resid 440 through 457 removed outlier: 3.551A pdb=" N LEU D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 478 removed outlier: 4.014A pdb=" N GLY D 478 " --> pdb=" O HIS D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 299 Processing helix chain 'E' and resid 317 through 331 Processing helix chain 'E' and resid 347 through 358 removed outlier: 3.517A pdb=" N GLU E 351 " --> pdb=" O GLU E 347 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU E 353 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN E 358 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 372 removed outlier: 4.008A pdb=" N ARG E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 384 removed outlier: 4.020A pdb=" N GLU E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 415 Processing helix chain 'E' and resid 440 through 457 removed outlier: 3.684A pdb=" N LEU E 445 " --> pdb=" O MET E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 478 removed outlier: 3.864A pdb=" N GLY E 478 " --> pdb=" O HIS E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 493 removed outlier: 4.286A pdb=" N LEU E 492 " --> pdb=" O SER E 489 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG E 493 " --> pdb=" O GLY E 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 489 through 493' Processing helix chain 'F' and resid 267 through 271 removed outlier: 3.698A pdb=" N SER F 270 " --> pdb=" O SER F 267 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU F 271 " --> pdb=" O ALA F 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 267 through 271' Processing helix chain 'F' and resid 274 through 280 Processing helix chain 'H' and resid 38 through 52 Processing helix chain 'H' and resid 64 through 75 removed outlier: 3.626A pdb=" N LYS H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 98 removed outlier: 3.611A pdb=" N ARG H 96 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU H 97 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 132 Processing helix chain 'H' and resid 139 through 150 Processing helix chain 'H' and resid 165 through 186 removed outlier: 3.698A pdb=" N LYS H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 231 removed outlier: 3.521A pdb=" N GLU H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS H 218 " --> pdb=" O VAL H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 246 Processing helix chain 'H' and resid 254 through 259 removed outlier: 4.047A pdb=" N GLU H 259 " --> pdb=" O ARG H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 348 Processing helix chain 'H' and resid 376 through 400 removed outlier: 3.709A pdb=" N GLN H 380 " --> pdb=" O ASP H 376 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA H 381 " --> pdb=" O PRO H 377 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP H 384 " --> pdb=" O GLN H 380 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 448 through 453 Processing helix chain 'H' and resid 479 through 488 Processing helix chain 'H' and resid 489 through 491 No H-bonds generated for 'chain 'H' and resid 489 through 491' Processing helix chain 'H' and resid 496 through 502 removed outlier: 3.895A pdb=" N ILE H 500 " --> pdb=" O TYR H 496 " (cutoff:3.500A) Processing helix chain 'H' and resid 504 through 514 removed outlier: 3.853A pdb=" N LYS H 508 " --> pdb=" O ASP H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 517 through 530 removed outlier: 3.566A pdb=" N TYR H 526 " --> pdb=" O LYS H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 537 through 542 removed outlier: 4.222A pdb=" N VAL H 541 " --> pdb=" O ILE H 537 " (cutoff:3.500A) Processing helix chain 'H' and resid 544 through 557 removed outlier: 3.579A pdb=" N GLU H 557 " --> pdb=" O LYS H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 561 through 573 Processing helix chain 'H' and resid 605 through 607 No H-bonds generated for 'chain 'H' and resid 605 through 607' Processing helix chain 'H' and resid 608 through 637 removed outlier: 4.232A pdb=" N SER H 616 " --> pdb=" O THR H 612 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA H 617 " --> pdb=" O LEU H 613 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU H 620 " --> pdb=" O SER H 616 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE H 621 " --> pdb=" O ALA H 617 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS H 622 " --> pdb=" O GLY H 618 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE H 627 " --> pdb=" O LYS H 623 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU H 630 " --> pdb=" O ILE H 626 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU H 633 " --> pdb=" O THR H 629 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU H 635 " --> pdb=" O GLU H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 662 through 684 removed outlier: 3.512A pdb=" N ALA H 666 " --> pdb=" O THR H 662 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLN H 674 " --> pdb=" O ILE H 670 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU H 675 " --> pdb=" O GLU H 671 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP H 684 " --> pdb=" O VAL H 680 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 15 removed outlier: 3.792A pdb=" N TYR A 13 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 26 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 77 Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142 removed outlier: 7.724A pdb=" N VAL A 176 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL A 154 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU A 178 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR A 156 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE A 153 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N MET A 205 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL A 155 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE A 202 " --> pdb=" O ARG A 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 267 removed outlier: 6.488A pdb=" N VAL B 337 " --> pdb=" O HIS B 392 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N TYR B 394 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU B 339 " --> pdb=" O TYR B 394 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE B 463 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU B 306 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL B 462 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE B 308 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B 307 " --> pdb=" O THR B 498 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE B 500 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N MET B 309 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU B 502 " --> pdb=" O MET B 309 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR B 311 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL B 516 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 392 removed outlier: 6.858A pdb=" N GLY A 338 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 421 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE A 463 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU A 423 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL A 307 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE A 500 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N MET A 309 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LEU A 502 " --> pdb=" O MET A 309 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N THR A 311 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ARG A 504 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 499 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL A 514 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TYR A 532 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL A 516 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 100 removed outlier: 3.700A pdb=" N SER B 120 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AA8, first strand: chain 'B' and resid 265 through 266 removed outlier: 3.795A pdb=" N LEU C 393 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C 337 " --> pdb=" O HIS C 392 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N TYR C 394 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU C 339 " --> pdb=" O TYR C 394 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY C 338 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE C 308 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE C 499 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 516 " --> pdb=" O GLY C 531 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY C 531 " --> pdb=" O VAL C 516 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE C 518 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE C 529 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 265 through 267 removed outlier: 6.647A pdb=" N VAL D 337 " --> pdb=" O HIS D 392 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N TYR D 394 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU D 339 " --> pdb=" O TYR D 394 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE D 308 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N CYS D 464 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N VAL D 310 " --> pdb=" O CYS D 464 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL D 307 " --> pdb=" O THR D 498 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE D 500 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N MET D 309 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU D 502 " --> pdb=" O MET D 309 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR D 311 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N ARG D 504 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL D 514 " --> pdb=" O TYR D 532 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR D 532 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL D 516 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU D 534 " --> pdb=" O GLU D 543 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 543 " --> pdb=" O GLU D 534 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 337 through 338 removed outlier: 4.258A pdb=" N ILE E 422 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE E 421 " --> pdb=" O VAL E 461 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE E 463 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU E 423 " --> pdb=" O ILE E 463 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS E 464 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL E 307 " --> pdb=" O THR E 498 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE E 500 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET E 309 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU E 502 " --> pdb=" O MET E 309 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N THR E 311 " --> pdb=" O LEU E 502 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL E 514 " --> pdb=" O TYR E 532 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR E 532 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL E 516 " --> pdb=" O ALA E 530 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 32 through 33 removed outlier: 6.821A pdb=" N ILE H 2 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE H 56 " --> pdb=" O ILE H 89 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 7 through 8 removed outlier: 6.758A pdb=" N GLU H 7 " --> pdb=" O HIS H 19 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 232 through 233 Processing sheet with id=AB5, first strand: chain 'H' and resid 264 through 267 Processing sheet with id=AB6, first strand: chain 'H' and resid 419 through 421 Processing sheet with id=AB7, first strand: chain 'H' and resid 646 through 651 removed outlier: 6.874A pdb=" N GLN H 657 " --> pdb=" O MET H 649 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 574 through 579 removed outlier: 4.057A pdb=" N SER H 576 " --> pdb=" O LYS H 587 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 592 through 594 635 hydrogen bonds defined for protein. 1830 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue (no planarity definition) Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 3.24 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3269 1.31 - 1.44: 5246 1.44 - 1.57: 11184 1.57 - 1.69: 80 1.69 - 1.82: 182 Bond restraints: 19961 Sorted by residual: bond pdb=" O3B TTP D 700 " pdb=" PG TTP D 700 " ideal model delta sigma weight residual 1.748 1.595 0.153 2.00e-02 2.50e+03 5.88e+01 bond pdb=" O3B TTP B 700 " pdb=" PG TTP B 700 " ideal model delta sigma weight residual 1.748 1.596 0.152 2.00e-02 2.50e+03 5.80e+01 bond pdb=" O3B TTP C 700 " pdb=" PG TTP C 700 " ideal model delta sigma weight residual 1.748 1.598 0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" O3B TTP E 700 " pdb=" PG TTP E 700 " ideal model delta sigma weight residual 1.748 1.599 0.149 2.00e-02 2.50e+03 5.56e+01 bond pdb=" O3B TTP H 801 " pdb=" PG TTP H 801 " ideal model delta sigma weight residual 1.748 1.600 0.148 2.00e-02 2.50e+03 5.48e+01 ... (remaining 19956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 26683 2.89 - 5.77: 268 5.77 - 8.66: 41 8.66 - 11.55: 19 11.55 - 14.43: 22 Bond angle restraints: 27033 Sorted by residual: angle pdb=" O4' DT T2036 " pdb=" C4' DT T2036 " pdb=" C3' DT T2036 " ideal model delta sigma weight residual 106.00 102.57 3.43 6.00e-01 2.78e+00 3.26e+01 angle pdb=" O4' DT T2037 " pdb=" C4' DT T2037 " pdb=" C3' DT T2037 " ideal model delta sigma weight residual 106.00 102.88 3.12 6.00e-01 2.78e+00 2.70e+01 angle pdb=" C2 TTP D 700 " pdb=" N3 TTP D 700 " pdb=" C4 TTP D 700 " ideal model delta sigma weight residual 128.28 113.85 14.43 3.00e+00 1.11e-01 2.31e+01 angle pdb=" C2 TTP C 700 " pdb=" N3 TTP C 700 " pdb=" C4 TTP C 700 " ideal model delta sigma weight residual 128.28 113.87 14.41 3.00e+00 1.11e-01 2.31e+01 angle pdb=" C2 TTP E 700 " pdb=" N3 TTP E 700 " pdb=" C4 TTP E 700 " ideal model delta sigma weight residual 128.28 113.87 14.41 3.00e+00 1.11e-01 2.31e+01 ... (remaining 27028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 11239 17.70 - 35.39: 487 35.39 - 53.08: 154 53.08 - 70.78: 49 70.78 - 88.47: 16 Dihedral angle restraints: 11945 sinusoidal: 5144 harmonic: 6801 Sorted by residual: dihedral pdb=" CA TYR H 64 " pdb=" C TYR H 64 " pdb=" N ASP H 65 " pdb=" CA ASP H 65 " ideal model delta harmonic sigma weight residual -180.00 -159.27 -20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ILE B 261 " pdb=" C ILE B 261 " pdb=" N PRO B 262 " pdb=" CA PRO B 262 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ILE A 261 " pdb=" C ILE A 261 " pdb=" N PRO A 262 " pdb=" CA PRO A 262 " ideal model delta harmonic sigma weight residual -180.00 -162.09 -17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 11942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2388 0.059 - 0.117: 479 0.117 - 0.176: 99 0.176 - 0.234: 7 0.234 - 0.293: 6 Chirality restraints: 2979 Sorted by residual: chirality pdb=" C4' TTP B 700 " pdb=" C3' TTP B 700 " pdb=" C5' TTP B 700 " pdb=" O4' TTP B 700 " both_signs ideal model delta sigma weight residual False -2.46 -2.75 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C4' TTP E 700 " pdb=" C3' TTP E 700 " pdb=" C5' TTP E 700 " pdb=" O4' TTP E 700 " both_signs ideal model delta sigma weight residual False -2.46 -2.72 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C4' TTP C 700 " pdb=" C3' TTP C 700 " pdb=" C5' TTP C 700 " pdb=" O4' TTP C 700 " both_signs ideal model delta sigma weight residual False -2.46 -2.71 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2976 not shown) Planarity restraints: 3346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET E 510 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO E 511 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 511 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 511 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 147 " -0.010 2.00e-02 2.50e+03 1.19e-02 3.57e+00 pdb=" CG TRP A 147 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 147 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 147 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 147 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 147 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 147 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 147 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 147 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 147 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 510 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO D 511 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 511 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 511 " 0.023 5.00e-02 4.00e+02 ... (remaining 3343 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 154 2.65 - 3.21: 15753 3.21 - 3.77: 28793 3.77 - 4.34: 39103 4.34 - 4.90: 63731 Nonbonded interactions: 147534 Sorted by model distance: nonbonded pdb=" OD2 ASP H 654 " pdb="MG MG H 802 " model vdw 2.082 2.170 nonbonded pdb=" OG SER B 319 " pdb="MG MG B 701 " model vdw 2.113 2.170 nonbonded pdb=" O1G TTP B 700 " pdb="MG MG B 701 " model vdw 2.115 2.170 nonbonded pdb=" O1B TTP C 700 " pdb="MG MG C 701 " model vdw 2.119 2.170 nonbonded pdb=" O1G TTP C 700 " pdb="MG MG C 701 " model vdw 2.157 2.170 ... (remaining 147529 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 65 through 549) selection = (chain 'B' and (resid 65 through 208 or resid 219 through 280 or resid 285 throu \ gh 430 or resid 437 through 549)) } ncs_group { reference = (chain 'C' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB )) or resid 441 through 545 or resid 700 through 701)) selection = (chain 'D' and (resid 285 through 373 or resid 377 through 395 or resid 404 thro \ ugh 429 or resid 439 through 506 or resid 510 through 545 or resid 700 through 7 \ 01)) selection = (chain 'E' and (resid 285 through 506 or resid 510 through 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.150 Find NCS groups from input model: 0.430 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.313 19967 Z= 0.303 Angle : 0.903 26.687 27041 Z= 0.471 Chirality : 0.051 0.293 2979 Planarity : 0.004 0.048 3346 Dihedral : 12.251 88.474 7590 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.10 % Allowed : 3.14 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -3.98 (0.13), residues: 2358 helix: -3.03 (0.11), residues: 831 sheet: -1.21 (0.25), residues: 412 loop : -2.86 (0.15), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 274 TYR 0.012 0.001 TYR H 203 PHE 0.020 0.001 PHE H 487 TRP 0.029 0.002 TRP A 147 HIS 0.006 0.001 HIS B 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.29 (19961) covalent geometry : angle 0.88071 / 0.47 (27033) SS BOND : bond 0.00064 / 0.03 ( 1) SS BOND : angle 1.38903 / 0.78 ( 2) hydrogen bonds : bond 0.16426 / 10.89 ( 648) hydrogen bonds : angle 7.06004 / 4.86 ( 1856) metal coordination : bond 0.20905 / 9.06 ( 4) metal coordination : angle 13.33768 / 5.85 ( 6) Misc. bond : bond 0.00078 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 621 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 TYR cc_start: 0.8392 (m-10) cc_final: 0.8056 (m-10) REVERT: A 107 GLN cc_start: 0.9268 (mt0) cc_final: 0.9033 (mt0) REVERT: A 142 PHE cc_start: 0.8341 (t80) cc_final: 0.8115 (t80) REVERT: A 147 TRP cc_start: 0.7737 (m-10) cc_final: 0.6989 (m-10) REVERT: A 148 ASN cc_start: 0.8691 (p0) cc_final: 0.8040 (m110) REVERT: A 187 LYS cc_start: 0.9331 (tppt) cc_final: 0.9125 (tptp) REVERT: A 251 MET cc_start: 0.8971 (mmm) cc_final: 0.8660 (ttp) REVERT: A 316 MET cc_start: 0.8407 (mmp) cc_final: 0.8076 (mmm) REVERT: A 329 TRP cc_start: 0.8380 (m-10) cc_final: 0.7481 (m-10) REVERT: A 379 ASP cc_start: 0.8744 (m-30) cc_final: 0.8031 (t0) REVERT: A 408 LYS cc_start: 0.9047 (mttp) cc_final: 0.8760 (mtpt) REVERT: A 419 ASP cc_start: 0.8179 (m-30) cc_final: 0.7819 (t70) REVERT: A 468 ASN cc_start: 0.8626 (m-40) cc_final: 0.8384 (t0) REVERT: B 142 PHE cc_start: 0.8352 (t80) cc_final: 0.7497 (t80) REVERT: B 162 MET cc_start: 0.8046 (tmm) cc_final: 0.7224 (tmm) REVERT: B 166 MET cc_start: 0.8722 (mtp) cc_final: 0.8225 (mtm) REVERT: B 180 HIS cc_start: 0.4725 (m170) cc_final: 0.3284 (m-70) REVERT: B 352 ASP cc_start: 0.8793 (m-30) cc_final: 0.8371 (m-30) REVERT: B 466 LEU cc_start: 0.9075 (mt) cc_final: 0.8834 (mt) REVERT: B 467 LYS cc_start: 0.9041 (pttt) cc_final: 0.8820 (ptpp) REVERT: B 484 THR cc_start: 0.9266 (p) cc_final: 0.9058 (t) REVERT: B 547 TYR cc_start: 0.8743 (t80) cc_final: 0.8439 (t80) REVERT: C 287 LEU cc_start: 0.8647 (tp) cc_final: 0.8439 (tp) REVERT: C 293 THR cc_start: 0.9044 (m) cc_final: 0.8827 (p) REVERT: C 333 MET cc_start: 0.8668 (mtt) cc_final: 0.8448 (mpp) REVERT: C 412 MET cc_start: 0.9128 (mtt) cc_final: 0.8793 (mtp) REVERT: C 443 ASP cc_start: 0.8969 (m-30) cc_final: 0.8444 (m-30) REVERT: D 314 SER cc_start: 0.8745 (m) cc_final: 0.8181 (t) REVERT: D 352 ASP cc_start: 0.8835 (t0) cc_final: 0.8388 (t0) REVERT: D 425 HIS cc_start: 0.8655 (t-90) cc_final: 0.8118 (t-90) REVERT: D 443 ASP cc_start: 0.7849 (m-30) cc_final: 0.7523 (m-30) REVERT: D 483 ILE cc_start: 0.9127 (tt) cc_final: 0.8583 (tt) REVERT: D 509 ASP cc_start: 0.7252 (p0) cc_final: 0.6888 (p0) REVERT: E 309 MET cc_start: 0.7957 (mmm) cc_final: 0.7494 (mpp) REVERT: E 339 LEU cc_start: 0.8988 (mm) cc_final: 0.8672 (mp) REVERT: E 341 MET cc_start: 0.6627 (mpm) cc_final: 0.6364 (mpp) REVERT: E 424 ASP cc_start: 0.6536 (t0) cc_final: 0.6130 (t70) REVERT: E 448 LYS cc_start: 0.9211 (ttmt) cc_final: 0.9001 (mmtm) REVERT: E 475 HIS cc_start: 0.4791 (m90) cc_final: 0.4200 (m170) REVERT: E 506 GLN cc_start: 0.8813 (tt0) cc_final: 0.8581 (mt0) REVERT: H 217 GLU cc_start: 0.8233 (tp30) cc_final: 0.7748 (tp30) REVERT: H 388 GLU cc_start: 0.8560 (tt0) cc_final: 0.8359 (tt0) REVERT: H 427 THR cc_start: 0.9393 (p) cc_final: 0.9033 (t) REVERT: H 483 CYS cc_start: 0.8567 (m) cc_final: 0.8327 (m) REVERT: H 553 LYS cc_start: 0.9557 (mmpt) cc_final: 0.9246 (mtmt) REVERT: H 626 ILE cc_start: 0.9597 (pt) cc_final: 0.9318 (tp) REVERT: H 649 MET cc_start: 0.8430 (mtm) cc_final: 0.7842 (mtm) outliers start: 2 outliers final: 0 residues processed: 623 average time/residue: 0.1523 time to fit residues: 139.6672 Evaluate side-chains 343 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 235 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 ASN A 129 ASN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN A 512 ASN B 67 ASN ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 244 ASN B 296 ASN B 465 HIS B 512 ASN C 296 ASN C 380 GLN C 475 HIS ** D 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN D 358 ASN ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 ASN E 325 GLN E 507 GLN E 512 ASN H 62 HIS H 398 GLN H 423 ASN H 432 HIS H 506 HIS H 615 GLN H 653 HIS H 683 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.078377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.060846 restraints weight = 80686.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.062860 restraints weight = 42833.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.064133 restraints weight = 27666.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 73)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.064981 restraints weight = 20663.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.065518 restraints weight = 16896.696| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19967 Z= 0.183 Angle : 0.690 16.735 27041 Z= 0.349 Chirality : 0.045 0.200 2979 Planarity : 0.004 0.047 3346 Dihedral : 11.767 97.414 3100 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.49 % Allowed : 14.29 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -2.60 (0.15), residues: 2358 helix: -1.15 (0.16), residues: 844 sheet: -0.99 (0.25), residues: 415 loop : -2.47 (0.16), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 493 TYR 0.018 0.001 TYR E 535 PHE 0.021 0.002 PHE H 120 TRP 0.028 0.002 TRP B 97 HIS 0.008 0.001 HIS H 704 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (19961) covalent geometry : angle 0.68382 / 0.35 (27033) SS BOND : bond 0.00064 / 0.03 ( 1) SS BOND : angle 1.91484 / 1.03 ( 2) hydrogen bonds : bond 0.04183 / 2.82 ( 648) hydrogen bonds : angle 5.18453 / 3.53 ( 1856) metal coordination : bond 0.00624 / 0.25 ( 4) metal coordination : angle 6.37937 / 3.15 ( 6) Misc. bond : bond 0.00071 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 328 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLN cc_start: 0.9325 (mt0) cc_final: 0.9112 (mt0) REVERT: A 147 TRP cc_start: 0.7829 (m-10) cc_final: 0.7332 (m-10) REVERT: A 148 ASN cc_start: 0.8573 (p0) cc_final: 0.8240 (m110) REVERT: A 316 MET cc_start: 0.8473 (mmp) cc_final: 0.8153 (mmm) REVERT: A 379 ASP cc_start: 0.8469 (m-30) cc_final: 0.8134 (t0) REVERT: A 425 HIS cc_start: 0.7691 (t70) cc_final: 0.7483 (t-170) REVERT: A 462 VAL cc_start: 0.8887 (t) cc_final: 0.8579 (m) REVERT: A 468 ASN cc_start: 0.8682 (m-40) cc_final: 0.8237 (t0) REVERT: B 142 PHE cc_start: 0.8434 (t80) cc_final: 0.7705 (t80) REVERT: B 162 MET cc_start: 0.8218 (tmm) cc_final: 0.7099 (tmm) REVERT: B 166 MET cc_start: 0.8722 (mtp) cc_final: 0.8317 (mtm) REVERT: B 411 TYR cc_start: 0.8609 (t80) cc_final: 0.8380 (t80) REVERT: B 467 LYS cc_start: 0.9139 (pttt) cc_final: 0.8764 (ptpp) REVERT: C 269 LEU cc_start: 0.9096 (pp) cc_final: 0.8871 (mt) REVERT: C 287 LEU cc_start: 0.8755 (tp) cc_final: 0.8472 (tp) REVERT: C 333 MET cc_start: 0.8643 (mtt) cc_final: 0.8417 (mpp) REVERT: C 341 MET cc_start: 0.9233 (mmt) cc_final: 0.8804 (mmp) REVERT: C 381 TRP cc_start: 0.9268 (m-10) cc_final: 0.9067 (m100) REVERT: C 424 ASP cc_start: 0.8753 (t0) cc_final: 0.8534 (t0) REVERT: C 430 VAL cc_start: 0.9144 (m) cc_final: 0.8860 (p) REVERT: C 443 ASP cc_start: 0.8936 (m-30) cc_final: 0.8464 (m-30) REVERT: D 309 MET cc_start: 0.9008 (mmm) cc_final: 0.8753 (mmm) REVERT: D 314 SER cc_start: 0.8726 (m) cc_final: 0.8511 (t) REVERT: D 352 ASP cc_start: 0.8839 (t0) cc_final: 0.8395 (t0) REVERT: D 425 HIS cc_start: 0.8557 (t-90) cc_final: 0.8028 (t-90) REVERT: D 470 ASP cc_start: 0.8250 (p0) cc_final: 0.7966 (p0) REVERT: E 289 PHE cc_start: 0.8363 (m-80) cc_final: 0.7856 (m-80) REVERT: E 341 MET cc_start: 0.7130 (mpm) cc_final: 0.5445 (mpp) REVERT: E 448 LYS cc_start: 0.9221 (ttmt) cc_final: 0.8990 (mmtm) REVERT: E 475 HIS cc_start: 0.4948 (m90) cc_final: 0.4447 (m90) REVERT: H 126 GLU cc_start: 0.8292 (mp0) cc_final: 0.7769 (tt0) REVERT: H 217 GLU cc_start: 0.8380 (tp30) cc_final: 0.7969 (tp30) REVERT: H 388 GLU cc_start: 0.8533 (tt0) cc_final: 0.8326 (tt0) REVERT: H 488 MET cc_start: 0.8651 (ptt) cc_final: 0.8400 (ttp) REVERT: H 649 MET cc_start: 0.8508 (mtm) cc_final: 0.7863 (mtm) outliers start: 50 outliers final: 27 residues processed: 355 average time/residue: 0.1328 time to fit residues: 74.1851 Evaluate side-chains 295 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 268 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain E residue 412 MET Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 464 CYS Chi-restraints excluded: chain H residue 439 GLN Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 629 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [23, 60, 160, 86, 70, 209, 134, 7, 171, 34, 190] chunk 23 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 7 optimal weight: 0.3980 chunk 171 optimal weight: 30.0000 chunk 34 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN B 67 ASN B 121 GLN ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 HIS B 465 HIS C 278 HIS C 325 GLN C 465 HIS ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 GLN E 507 GLN ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 558 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.075701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.058222 restraints weight = 84432.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.060048 restraints weight = 46383.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.061229 restraints weight = 30791.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.062004 restraints weight = 23449.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.062554 restraints weight = 19528.292| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19967 Z= 0.215 Angle : 0.679 11.355 27041 Z= 0.346 Chirality : 0.045 0.211 2979 Planarity : 0.004 0.048 3346 Dihedral : 11.794 108.293 3100 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.14 % Allowed : 14.49 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.91 (0.16), residues: 2358 helix: -0.26 (0.18), residues: 867 sheet: -0.91 (0.25), residues: 420 loop : -2.27 (0.17), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 404 TYR 0.018 0.002 TYR E 535 PHE 0.031 0.002 PHE H 686 TRP 0.018 0.002 TRP A 147 HIS 0.008 0.001 HIS H 704 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (19961) covalent geometry : angle 0.67288 / 0.35 (27033) SS BOND : bond 0.03241 / 1.71 ( 1) SS BOND : angle 0.81531 / 0.44 ( 2) hydrogen bonds : bond 0.03858 / 2.58 ( 648) hydrogen bonds : angle 4.93355 / 3.34 ( 1856) metal coordination : bond 0.01031 / 0.45 ( 4) metal coordination : angle 6.06387 / 2.86 ( 6) Misc. bond : bond 0.00119 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 261 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 GLN cc_start: 0.9371 (OUTLIER) cc_final: 0.9033 (mt0) REVERT: A 147 TRP cc_start: 0.8238 (m-10) cc_final: 0.7731 (m-10) REVERT: A 269 LEU cc_start: 0.8780 (mt) cc_final: 0.8579 (mt) REVERT: A 316 MET cc_start: 0.8532 (mmp) cc_final: 0.8228 (mmm) REVERT: A 347 GLU cc_start: 0.8800 (pm20) cc_final: 0.8458 (pm20) REVERT: A 379 ASP cc_start: 0.8486 (m-30) cc_final: 0.7981 (t70) REVERT: A 425 HIS cc_start: 0.7588 (t70) cc_final: 0.7059 (t-170) REVERT: A 468 ASN cc_start: 0.8646 (m-40) cc_final: 0.8181 (t0) REVERT: A 485 ASP cc_start: 0.7852 (m-30) cc_final: 0.7542 (m-30) REVERT: B 142 PHE cc_start: 0.8390 (t80) cc_final: 0.7591 (t80) REVERT: B 162 MET cc_start: 0.8280 (tmm) cc_final: 0.7353 (tmm) REVERT: B 166 MET cc_start: 0.8728 (mtp) cc_final: 0.8363 (mtm) REVERT: B 251 MET cc_start: 0.9240 (mmt) cc_final: 0.9023 (mmm) REVERT: B 467 LYS cc_start: 0.9163 (pttt) cc_final: 0.8772 (ptpp) REVERT: C 287 LEU cc_start: 0.8853 (tp) cc_final: 0.8341 (tp) REVERT: C 341 MET cc_start: 0.9231 (mmt) cc_final: 0.8921 (mmp) REVERT: C 430 VAL cc_start: 0.9424 (m) cc_final: 0.9148 (p) REVERT: C 443 ASP cc_start: 0.8882 (m-30) cc_final: 0.8412 (m-30) REVERT: D 307 VAL cc_start: 0.8129 (t) cc_final: 0.7913 (m) REVERT: D 314 SER cc_start: 0.8842 (m) cc_final: 0.8566 (t) REVERT: D 352 ASP cc_start: 0.8831 (t0) cc_final: 0.8407 (t0) REVERT: D 425 HIS cc_start: 0.8588 (t-90) cc_final: 0.8031 (t-90) REVERT: D 533 MET cc_start: 0.8138 (mpp) cc_final: 0.7829 (mpp) REVERT: E 289 PHE cc_start: 0.8298 (m-80) cc_final: 0.7783 (m-80) REVERT: E 309 MET cc_start: 0.8259 (mmm) cc_final: 0.7832 (mpp) REVERT: E 475 HIS cc_start: 0.4252 (m90) cc_final: 0.4046 (m170) REVERT: E 533 MET cc_start: 0.3074 (mmm) cc_final: 0.2873 (mmm) REVERT: H 120 PHE cc_start: 0.8749 (t80) cc_final: 0.8417 (t80) REVERT: H 217 GLU cc_start: 0.8582 (tp30) cc_final: 0.8176 (tp30) REVERT: H 649 MET cc_start: 0.8556 (mtm) cc_final: 0.8190 (mtm) outliers start: 63 outliers final: 42 residues processed: 309 average time/residue: 0.1286 time to fit residues: 63.5256 Evaluate side-chains 284 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain E residue 380 GLN Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 464 CYS Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 259 GLU Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 419 SER Chi-restraints excluded: chain H residue 439 GLN Chi-restraints excluded: chain H residue 483 CYS Chi-restraints excluded: chain H residue 537 ILE Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 629 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [208, 116, 34, 189, 235, 16, 238, 190, 230, 109, 183] chunk 208 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 238 optimal weight: 20.0000 chunk 190 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 465 HIS ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 507 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.076752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.059076 restraints weight = 83512.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.060907 restraints weight = 45869.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.062151 restraints weight = 30582.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.062950 restraints weight = 23184.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.063466 restraints weight = 19231.317| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19967 Z= 0.115 Angle : 0.609 11.408 27041 Z= 0.301 Chirality : 0.043 0.165 2979 Planarity : 0.003 0.038 3346 Dihedral : 11.640 110.753 3100 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.44 % Allowed : 15.14 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.58 (0.17), residues: 2358 helix: 0.07 (0.18), residues: 861 sheet: -0.79 (0.26), residues: 419 loop : -2.09 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 303 TYR 0.021 0.001 TYR H 130 PHE 0.015 0.001 PHE H 120 TRP 0.033 0.001 TRP C 381 HIS 0.006 0.001 HIS H 704 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (19961) covalent geometry : angle 0.60456 / 0.30 (27033) SS BOND : bond 0.00952 / 0.50 ( 1) SS BOND : angle 0.77351 / 0.44 ( 2) hydrogen bonds : bond 0.03245 / 2.19 ( 648) hydrogen bonds : angle 4.66393 / 3.16 ( 1856) metal coordination : bond 0.00679 / 0.28 ( 4) metal coordination : angle 4.75074 / 2.32 ( 6) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 274 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 SER cc_start: 0.9308 (m) cc_final: 0.8859 (t) REVERT: A 147 TRP cc_start: 0.8096 (m-10) cc_final: 0.7598 (m-10) REVERT: A 316 MET cc_start: 0.8529 (mmp) cc_final: 0.8212 (mmm) REVERT: A 341 MET cc_start: 0.6708 (tpp) cc_final: 0.5575 (tpp) REVERT: A 347 GLU cc_start: 0.8800 (pm20) cc_final: 0.8594 (pm20) REVERT: A 379 ASP cc_start: 0.8509 (m-30) cc_final: 0.8023 (t70) REVERT: A 468 ASN cc_start: 0.8637 (m-40) cc_final: 0.8177 (t0) REVERT: A 485 ASP cc_start: 0.7913 (m-30) cc_final: 0.7616 (m-30) REVERT: B 142 PHE cc_start: 0.8403 (t80) cc_final: 0.7534 (t80) REVERT: B 162 MET cc_start: 0.8298 (tmm) cc_final: 0.7441 (tmm) REVERT: B 166 MET cc_start: 0.8728 (mtp) cc_final: 0.8436 (mtm) REVERT: B 309 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7932 (tpt) REVERT: B 467 LYS cc_start: 0.9160 (pttt) cc_final: 0.8772 (ptpp) REVERT: B 533 MET cc_start: 0.7941 (mmm) cc_final: 0.7721 (mmm) REVERT: C 333 MET cc_start: 0.8751 (mpp) cc_final: 0.8324 (mpp) REVERT: C 341 MET cc_start: 0.9272 (mmt) cc_final: 0.8837 (mmp) REVERT: C 344 GLU cc_start: 0.7710 (pm20) cc_final: 0.7418 (pm20) REVERT: C 406 LEU cc_start: 0.9033 (pp) cc_final: 0.8739 (pp) REVERT: C 424 ASP cc_start: 0.8812 (t0) cc_final: 0.8514 (t0) REVERT: C 443 ASP cc_start: 0.8809 (m-30) cc_final: 0.8379 (m-30) REVERT: D 314 SER cc_start: 0.8780 (m) cc_final: 0.8524 (t) REVERT: D 352 ASP cc_start: 0.8800 (t0) cc_final: 0.8378 (t0) REVERT: D 425 HIS cc_start: 0.8572 (t-90) cc_final: 0.7985 (t-90) REVERT: D 533 MET cc_start: 0.8126 (mpp) cc_final: 0.7811 (mpp) REVERT: E 289 PHE cc_start: 0.8340 (m-80) cc_final: 0.7860 (m-80) REVERT: E 309 MET cc_start: 0.8217 (mmm) cc_final: 0.8008 (mpp) REVERT: E 448 LYS cc_start: 0.9193 (ttmt) cc_final: 0.8933 (mmtm) REVERT: F 273 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8332 (tp30) REVERT: H 88 CYS cc_start: 0.8771 (p) cc_final: 0.8442 (t) REVERT: H 120 PHE cc_start: 0.8652 (t80) cc_final: 0.8350 (t80) REVERT: H 217 GLU cc_start: 0.8592 (tp30) cc_final: 0.8152 (tp30) REVERT: H 649 MET cc_start: 0.8563 (mtm) cc_final: 0.8207 (mtm) outliers start: 49 outliers final: 34 residues processed: 307 average time/residue: 0.1319 time to fit residues: 64.4118 Evaluate side-chains 276 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 464 CYS Chi-restraints excluded: chain E residue 524 THR Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 259 GLU Chi-restraints excluded: chain H residue 265 TYR Chi-restraints excluded: chain H residue 537 ILE Chi-restraints excluded: chain H residue 629 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [47, 115, 18, 197, 239, 125, 193, 206, 225, 78, 153] chunk 47 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS B 114 GLN ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 HIS C 358 ASN ** D 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 ASN E 494 GLN E 512 ASN F 278 HIS ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 611 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.072236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.054709 restraints weight = 86435.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.056430 restraints weight = 47888.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.057503 restraints weight = 32000.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.058209 restraints weight = 24606.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.058641 restraints weight = 20747.083| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 19967 Z= 0.306 Angle : 0.788 12.537 27041 Z= 0.396 Chirality : 0.047 0.214 2979 Planarity : 0.005 0.064 3346 Dihedral : 12.037 120.995 3100 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.88 % Allowed : 14.79 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.51 (0.17), residues: 2358 helix: 0.12 (0.18), residues: 880 sheet: -0.94 (0.26), residues: 412 loop : -1.99 (0.17), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 35 TYR 0.021 0.002 TYR A 96 PHE 0.019 0.002 PHE A 452 TRP 0.060 0.002 TRP C 381 HIS 0.009 0.002 HIS E 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.31 (19961) covalent geometry : angle 0.78244 / 0.40 (27033) SS BOND : bond 0.00087 / 0.05 ( 1) SS BOND : angle 1.36472 / 0.79 ( 2) hydrogen bonds : bond 0.04322 / 2.93 ( 648) hydrogen bonds : angle 5.11882 / 3.46 ( 1856) metal coordination : bond 0.01238 / 0.56 ( 4) metal coordination : angle 6.27998 / 2.94 ( 6) Misc. bond : bond 0.00171 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 233 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 SER cc_start: 0.9271 (m) cc_final: 0.8871 (t) REVERT: A 269 LEU cc_start: 0.8793 (mt) cc_final: 0.8538 (mt) REVERT: A 316 MET cc_start: 0.8496 (mmp) cc_final: 0.8202 (mmm) REVERT: A 347 GLU cc_start: 0.8859 (pm20) cc_final: 0.8584 (pm20) REVERT: A 379 ASP cc_start: 0.8621 (m-30) cc_final: 0.8066 (t70) REVERT: A 468 ASN cc_start: 0.8606 (m-40) cc_final: 0.8029 (t0) REVERT: A 485 ASP cc_start: 0.7848 (m-30) cc_final: 0.7515 (m-30) REVERT: B 131 LYS cc_start: 0.8747 (mppt) cc_final: 0.8493 (mppt) REVERT: B 260 TRP cc_start: 0.8087 (t-100) cc_final: 0.7883 (t-100) REVERT: B 411 TYR cc_start: 0.8785 (t80) cc_final: 0.8538 (t80) REVERT: B 467 LYS cc_start: 0.9177 (pttt) cc_final: 0.8955 (ptpp) REVERT: C 333 MET cc_start: 0.8760 (mpp) cc_final: 0.8052 (mpp) REVERT: C 341 MET cc_start: 0.9293 (mmt) cc_final: 0.8941 (mmp) REVERT: C 344 GLU cc_start: 0.8023 (pm20) cc_final: 0.7730 (pm20) REVERT: C 443 ASP cc_start: 0.8946 (m-30) cc_final: 0.8558 (m-30) REVERT: D 314 SER cc_start: 0.8894 (m) cc_final: 0.8632 (t) REVERT: D 351 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8498 (mt-10) REVERT: D 352 ASP cc_start: 0.8843 (t0) cc_final: 0.8394 (t0) REVERT: D 425 HIS cc_start: 0.8600 (t-90) cc_final: 0.8084 (t70) REVERT: D 533 MET cc_start: 0.8089 (mpp) cc_final: 0.7833 (mpp) REVERT: E 289 PHE cc_start: 0.8387 (m-80) cc_final: 0.7763 (m-80) REVERT: E 309 MET cc_start: 0.8283 (mmm) cc_final: 0.8081 (mmm) REVERT: E 348 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: E 448 LYS cc_start: 0.9222 (ttmt) cc_final: 0.8985 (mmtm) REVERT: E 494 GLN cc_start: 0.6506 (mm110) cc_final: 0.6232 (mp10) REVERT: H 217 GLU cc_start: 0.8743 (tp30) cc_final: 0.8387 (tp30) REVERT: H 439 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8453 (tt0) REVERT: H 488 MET cc_start: 0.8671 (ttp) cc_final: 0.8462 (ttt) REVERT: H 649 MET cc_start: 0.8569 (mtm) cc_final: 0.8036 (mtm) outliers start: 78 outliers final: 51 residues processed: 289 average time/residue: 0.1319 time to fit residues: 60.2464 Evaluate side-chains 266 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 213 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 464 CYS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 265 TYR Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 439 GLN Chi-restraints excluded: chain H residue 487 PHE Chi-restraints excluded: chain H residue 537 ILE Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 629 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [25, 80, 172, 204, 179, 20, 192, 148, 92, 39, 218] chunk 25 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 192 optimal weight: 0.0030 chunk 148 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 218 optimal weight: 0.7980 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.074054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.056288 restraints weight = 84021.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.058069 restraints weight = 46456.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059233 restraints weight = 30882.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.059962 restraints weight = 23513.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.060475 restraints weight = 19687.726| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19967 Z= 0.131 Angle : 0.618 12.617 27041 Z= 0.309 Chirality : 0.044 0.262 2979 Planarity : 0.003 0.064 3346 Dihedral : 11.794 118.780 3100 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.79 % Allowed : 16.63 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.21 (0.17), residues: 2358 helix: 0.43 (0.18), residues: 870 sheet: -0.85 (0.26), residues: 410 loop : -1.83 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 35 TYR 0.013 0.001 TYR H 203 PHE 0.027 0.001 PHE H 163 TRP 0.026 0.001 TRP C 381 HIS 0.006 0.001 HIS C 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (19961) covalent geometry : angle 0.61374 / 0.31 (27033) SS BOND : bond 0.00178 / 0.09 ( 1) SS BOND : angle 1.21214 / 0.69 ( 2) hydrogen bonds : bond 0.03475 / 2.35 ( 648) hydrogen bonds : angle 4.66825 / 3.16 ( 1856) metal coordination : bond 0.00636 / 0.26 ( 4) metal coordination : angle 4.95255 / 2.45 ( 6) Misc. bond : bond 0.00062 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 240 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 SER cc_start: 0.9260 (m) cc_final: 0.8850 (t) REVERT: A 269 LEU cc_start: 0.8660 (mt) cc_final: 0.8444 (mt) REVERT: A 307 VAL cc_start: 0.8807 (t) cc_final: 0.8554 (p) REVERT: A 316 MET cc_start: 0.8471 (mmp) cc_final: 0.8165 (mmm) REVERT: A 379 ASP cc_start: 0.8586 (m-30) cc_final: 0.8110 (t70) REVERT: A 468 ASN cc_start: 0.8628 (m-40) cc_final: 0.8044 (t0) REVERT: A 485 ASP cc_start: 0.7912 (m-30) cc_final: 0.7586 (m-30) REVERT: A 533 MET cc_start: 0.8280 (mtt) cc_final: 0.8009 (mmt) REVERT: B 127 ASP cc_start: 0.9139 (m-30) cc_final: 0.8773 (p0) REVERT: B 142 PHE cc_start: 0.8627 (t80) cc_final: 0.7935 (t80) REVERT: B 411 TYR cc_start: 0.8762 (t80) cc_final: 0.8472 (t80) REVERT: B 467 LYS cc_start: 0.9139 (pttt) cc_final: 0.8921 (ptpp) REVERT: C 333 MET cc_start: 0.8850 (mpp) cc_final: 0.8018 (mpp) REVERT: C 341 MET cc_start: 0.9281 (mmt) cc_final: 0.8867 (mmp) REVERT: C 344 GLU cc_start: 0.7955 (pm20) cc_final: 0.7591 (pm20) REVERT: C 424 ASP cc_start: 0.8880 (t0) cc_final: 0.8604 (t0) REVERT: C 443 ASP cc_start: 0.8801 (m-30) cc_final: 0.8432 (m-30) REVERT: D 309 MET cc_start: 0.9046 (mmm) cc_final: 0.8789 (mmm) REVERT: D 314 SER cc_start: 0.8867 (m) cc_final: 0.8607 (t) REVERT: D 351 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8436 (mt-10) REVERT: D 352 ASP cc_start: 0.8790 (t0) cc_final: 0.8357 (t0) REVERT: D 412 MET cc_start: 0.8674 (mmt) cc_final: 0.8438 (mmm) REVERT: D 425 HIS cc_start: 0.8408 (t-90) cc_final: 0.7981 (t-90) REVERT: D 533 MET cc_start: 0.8054 (mpp) cc_final: 0.7801 (mpp) REVERT: E 289 PHE cc_start: 0.8428 (m-80) cc_final: 0.7910 (m-80) REVERT: E 348 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: E 448 LYS cc_start: 0.9199 (ttmt) cc_final: 0.8924 (mmtm) REVERT: F 273 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8605 (tp30) REVERT: F 274 ARG cc_start: 0.8134 (ptp-110) cc_final: 0.7864 (ptp-170) REVERT: H 126 GLU cc_start: 0.8405 (mp0) cc_final: 0.7976 (tt0) REVERT: H 217 GLU cc_start: 0.8675 (tp30) cc_final: 0.8279 (tp30) REVERT: H 488 MET cc_start: 0.8582 (ttp) cc_final: 0.8347 (ttt) REVERT: H 649 MET cc_start: 0.8577 (mtm) cc_final: 0.7945 (mtm) outliers start: 56 outliers final: 41 residues processed: 281 average time/residue: 0.1257 time to fit residues: 57.1345 Evaluate side-chains 269 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 464 CYS Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 265 TYR Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 396 ILE Chi-restraints excluded: chain H residue 419 SER Chi-restraints excluded: chain H residue 487 PHE Chi-restraints excluded: chain H residue 537 ILE Chi-restraints excluded: chain H residue 629 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [64, 77, 116, 98, 63, 53, 205, 46, 106, 19, 93] chunk 64 optimal weight: 50.0000 chunk 77 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 GLN ** E 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 494 GLN ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 460 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.069963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.052445 restraints weight = 88008.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.054090 restraints weight = 48148.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.055144 restraints weight = 32331.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.055820 restraints weight = 24842.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.056302 restraints weight = 20975.218| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 19967 Z= 0.373 Angle : 0.870 15.658 27041 Z= 0.436 Chirality : 0.050 0.261 2979 Planarity : 0.005 0.050 3346 Dihedral : 12.229 120.443 3100 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.64 % Allowed : 16.93 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.67 (0.17), residues: 2358 helix: -0.04 (0.17), residues: 881 sheet: -0.99 (0.27), residues: 396 loop : -2.05 (0.17), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 363 TYR 0.018 0.003 TYR A 37 PHE 0.024 0.003 PHE A 452 TRP 0.069 0.003 TRP C 381 HIS 0.009 0.002 HIS E 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00796 / 0.37 (19961) covalent geometry : angle 0.86379 / 0.44 (27033) SS BOND : bond 0.00526 / 0.28 ( 1) SS BOND : angle 1.49636 / 0.87 ( 2) hydrogen bonds : bond 0.04901 / 3.31 ( 648) hydrogen bonds : angle 5.34447 / 3.61 ( 1856) metal coordination : bond 0.01431 / 0.65 ( 4) metal coordination : angle 6.95756 / 3.26 ( 6) Misc. bond : bond 0.00201 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 216 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 SER cc_start: 0.9247 (m) cc_final: 0.8856 (t) REVERT: A 269 LEU cc_start: 0.8746 (mt) cc_final: 0.8462 (mt) REVERT: A 316 MET cc_start: 0.8611 (mmp) cc_final: 0.8307 (mmm) REVERT: A 379 ASP cc_start: 0.8685 (m-30) cc_final: 0.8155 (t70) REVERT: A 438 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8064 (mm-30) REVERT: A 468 ASN cc_start: 0.8664 (m-40) cc_final: 0.7975 (t0) REVERT: A 533 MET cc_start: 0.8590 (mtt) cc_final: 0.8337 (mmt) REVERT: B 142 PHE cc_start: 0.8753 (t80) cc_final: 0.8403 (t80) REVERT: B 467 LYS cc_start: 0.9131 (pttt) cc_final: 0.8885 (ptpp) REVERT: C 333 MET cc_start: 0.8816 (mpp) cc_final: 0.7851 (mpp) REVERT: C 341 MET cc_start: 0.9305 (mmt) cc_final: 0.8922 (mmp) REVERT: C 344 GLU cc_start: 0.8220 (pm20) cc_final: 0.7945 (pm20) REVERT: C 403 ASP cc_start: 0.9381 (m-30) cc_final: 0.9030 (m-30) REVERT: C 443 ASP cc_start: 0.8866 (m-30) cc_final: 0.8477 (m-30) REVERT: D 309 MET cc_start: 0.8924 (mmm) cc_final: 0.8687 (mmm) REVERT: D 351 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8461 (mt-10) REVERT: D 352 ASP cc_start: 0.8847 (t0) cc_final: 0.8394 (t0) REVERT: D 425 HIS cc_start: 0.8610 (t-90) cc_final: 0.8132 (t-90) REVERT: D 446 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8734 (ttp) REVERT: D 471 LYS cc_start: 0.8433 (tptp) cc_final: 0.7928 (mmmt) REVERT: D 510 MET cc_start: 0.7969 (pmm) cc_final: 0.7696 (pmm) REVERT: D 537 LYS cc_start: 0.8373 (mmmt) cc_final: 0.8123 (mttm) REVERT: E 289 PHE cc_start: 0.8460 (m-80) cc_final: 0.7851 (m-80) REVERT: E 347 GLU cc_start: 0.8996 (mp0) cc_final: 0.8776 (pm20) REVERT: E 348 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: E 448 LYS cc_start: 0.9231 (ttmt) cc_final: 0.9031 (mmtm) REVERT: H 217 GLU cc_start: 0.8868 (tp30) cc_final: 0.8535 (tp30) REVERT: H 439 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8633 (tt0) REVERT: H 488 MET cc_start: 0.8627 (ttp) cc_final: 0.8422 (ttt) REVERT: H 649 MET cc_start: 0.8650 (mtm) cc_final: 0.7994 (mtm) outliers start: 73 outliers final: 59 residues processed: 266 average time/residue: 0.1282 time to fit residues: 55.1706 Evaluate side-chains 267 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 205 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 380 GLN Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 464 CYS Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 265 TYR Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 439 GLN Chi-restraints excluded: chain H residue 440 ILE Chi-restraints excluded: chain H residue 487 PHE Chi-restraints excluded: chain H residue 537 ILE Chi-restraints excluded: chain H residue 629 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [45, 38, 129, 95, 141, 20, 40, 84, 62, 0, 117] chunk 45 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 84 optimal weight: 0.0770 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.072696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.054934 restraints weight = 84560.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.056711 restraints weight = 45145.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.057860 restraints weight = 29847.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058610 restraints weight = 22663.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.059063 restraints weight = 18888.334| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19967 Z= 0.128 Angle : 0.665 12.977 27041 Z= 0.333 Chirality : 0.045 0.244 2979 Planarity : 0.003 0.052 3346 Dihedral : 11.881 120.692 3100 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.39 % Allowed : 18.82 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.20 (0.17), residues: 2358 helix: 0.45 (0.18), residues: 866 sheet: -0.89 (0.27), residues: 394 loop : -1.78 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 504 TYR 0.014 0.001 TYR H 389 PHE 0.021 0.002 PHE H 163 TRP 0.038 0.002 TRP C 381 HIS 0.005 0.001 HIS C 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (19961) covalent geometry : angle 0.66138 / 0.33 (27033) SS BOND : bond 0.00165 / 0.09 ( 1) SS BOND : angle 1.45557 / 0.83 ( 2) hydrogen bonds : bond 0.03647 / 2.45 ( 648) hydrogen bonds : angle 4.70438 / 3.17 ( 1856) metal coordination : bond 0.00557 / 0.23 ( 4) metal coordination : angle 4.94973 / 2.49 ( 6) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 236 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.9050 (mmm) cc_final: 0.8842 (mmp) REVERT: A 138 SER cc_start: 0.9263 (m) cc_final: 0.8847 (t) REVERT: A 148 ASN cc_start: 0.8586 (p0) cc_final: 0.8175 (m110) REVERT: A 269 LEU cc_start: 0.8720 (mt) cc_final: 0.8478 (mt) REVERT: A 316 MET cc_start: 0.8593 (mmp) cc_final: 0.8168 (mmm) REVERT: A 379 ASP cc_start: 0.8651 (m-30) cc_final: 0.8067 (t70) REVERT: A 468 ASN cc_start: 0.8597 (m-40) cc_final: 0.7940 (t0) REVERT: B 467 LYS cc_start: 0.9155 (pttt) cc_final: 0.8898 (ptpp) REVERT: C 333 MET cc_start: 0.8966 (mpp) cc_final: 0.8025 (mpp) REVERT: C 341 MET cc_start: 0.9328 (mmt) cc_final: 0.8892 (mmp) REVERT: C 344 GLU cc_start: 0.8102 (pm20) cc_final: 0.7730 (pm20) REVERT: C 424 ASP cc_start: 0.8956 (t0) cc_final: 0.8731 (t0) REVERT: C 443 ASP cc_start: 0.8745 (m-30) cc_final: 0.8400 (m-30) REVERT: D 351 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8387 (mt-10) REVERT: D 352 ASP cc_start: 0.8745 (t0) cc_final: 0.8324 (t0) REVERT: D 412 MET cc_start: 0.8885 (mmp) cc_final: 0.8667 (mmp) REVERT: D 425 HIS cc_start: 0.8410 (t-90) cc_final: 0.7990 (t-90) REVERT: D 446 MET cc_start: 0.8924 (tpp) cc_final: 0.8656 (ttt) REVERT: D 471 LYS cc_start: 0.8449 (tptp) cc_final: 0.7963 (mmmt) REVERT: D 533 MET cc_start: 0.8015 (mpp) cc_final: 0.7723 (mpp) REVERT: E 289 PHE cc_start: 0.8436 (m-80) cc_final: 0.7944 (m-80) REVERT: E 348 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: E 377 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6721 (ptpp) REVERT: E 448 LYS cc_start: 0.9215 (ttmt) cc_final: 0.8959 (mmtm) REVERT: H 125 LEU cc_start: 0.8504 (tp) cc_final: 0.8267 (tp) REVERT: H 126 GLU cc_start: 0.8302 (mp0) cc_final: 0.8053 (tt0) REVERT: H 217 GLU cc_start: 0.8782 (tp30) cc_final: 0.8378 (tp30) REVERT: H 649 MET cc_start: 0.8660 (mtm) cc_final: 0.7935 (mtm) outliers start: 48 outliers final: 40 residues processed: 272 average time/residue: 0.1276 time to fit residues: 55.6100 Evaluate side-chains 261 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 219 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 464 CYS Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 265 TYR Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 396 ILE Chi-restraints excluded: chain H residue 487 PHE Chi-restraints excluded: chain H residue 537 ILE Chi-restraints excluded: chain H residue 555 PHE Chi-restraints excluded: chain H residue 629 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [10, 164, 151, 222, 226, 150, 65, 70, 139, 223, 178] chunk 10 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.070786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.053304 restraints weight = 85735.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.054921 restraints weight = 47847.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.055951 restraints weight = 32243.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.056660 restraints weight = 24910.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.057119 restraints weight = 20974.976| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 19967 Z= 0.276 Angle : 0.762 11.672 27041 Z= 0.383 Chirality : 0.047 0.226 2979 Planarity : 0.004 0.038 3346 Dihedral : 12.069 119.521 3100 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.59 % Allowed : 18.92 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.30 (0.17), residues: 2358 helix: 0.37 (0.18), residues: 874 sheet: -0.95 (0.27), residues: 396 loop : -1.86 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 359 TYR 0.022 0.002 TYR H 130 PHE 0.017 0.002 PHE H 163 TRP 0.070 0.002 TRP C 381 HIS 0.009 0.002 HIS C 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.28 (19961) covalent geometry : angle 0.75724 / 0.38 (27033) SS BOND : bond 0.00845 / 0.44 ( 1) SS BOND : angle 1.61538 / 0.94 ( 2) hydrogen bonds : bond 0.04218 / 2.86 ( 648) hydrogen bonds : angle 5.10644 / 3.43 ( 1856) metal coordination : bond 0.01039 / 0.46 ( 4) metal coordination : angle 5.67693 / 2.71 ( 6) Misc. bond : bond 0.00191 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 216 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 SER cc_start: 0.9289 (m) cc_final: 0.8891 (t) REVERT: A 269 LEU cc_start: 0.8745 (mt) cc_final: 0.8441 (mt) REVERT: A 316 MET cc_start: 0.8625 (mmp) cc_final: 0.8278 (mmm) REVERT: A 379 ASP cc_start: 0.8703 (m-30) cc_final: 0.8089 (t70) REVERT: A 425 HIS cc_start: 0.6638 (t-170) cc_final: 0.6084 (t-90) REVERT: A 468 ASN cc_start: 0.8604 (m-40) cc_final: 0.7926 (t0) REVERT: B 467 LYS cc_start: 0.9131 (pttt) cc_final: 0.8880 (ptpp) REVERT: C 333 MET cc_start: 0.8928 (mpp) cc_final: 0.7969 (mpp) REVERT: C 341 MET cc_start: 0.9310 (mmt) cc_final: 0.8929 (mmp) REVERT: C 344 GLU cc_start: 0.8223 (pm20) cc_final: 0.7948 (pm20) REVERT: C 443 ASP cc_start: 0.8775 (m-30) cc_final: 0.8438 (m-30) REVERT: D 351 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8440 (mt-10) REVERT: D 352 ASP cc_start: 0.8805 (t0) cc_final: 0.8361 (t0) REVERT: D 412 MET cc_start: 0.8951 (mmp) cc_final: 0.8727 (mmp) REVERT: D 425 HIS cc_start: 0.8509 (t-90) cc_final: 0.8054 (t-90) REVERT: D 471 LYS cc_start: 0.8487 (tptp) cc_final: 0.8015 (mmmt) REVERT: D 533 MET cc_start: 0.8037 (mpp) cc_final: 0.7772 (mpp) REVERT: D 537 LYS cc_start: 0.8430 (mttm) cc_final: 0.7922 (mttm) REVERT: E 289 PHE cc_start: 0.8537 (m-80) cc_final: 0.7927 (m-80) REVERT: E 348 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: E 448 LYS cc_start: 0.9235 (ttmt) cc_final: 0.8966 (mmtm) REVERT: H 217 GLU cc_start: 0.8826 (tp30) cc_final: 0.8477 (tp30) REVERT: H 649 MET cc_start: 0.8560 (mtm) cc_final: 0.7899 (mtm) outliers start: 52 outliers final: 46 residues processed: 255 average time/residue: 0.1246 time to fit residues: 50.9255 Evaluate side-chains 257 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 464 CYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 265 TYR Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 487 PHE Chi-restraints excluded: chain H residue 537 ILE Chi-restraints excluded: chain H residue 555 PHE Chi-restraints excluded: chain H residue 629 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [188, 132, 191, 49, 31, 129, 239, 40, 194, 114, 8] chunk 188 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 239 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.072064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.054465 restraints weight = 84423.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.056124 restraints weight = 46231.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.057242 restraints weight = 31054.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.057948 restraints weight = 23710.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.058415 restraints weight = 19926.899| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19967 Z= 0.157 Angle : 0.687 12.327 27041 Z= 0.344 Chirality : 0.046 0.496 2979 Planarity : 0.003 0.039 3346 Dihedral : 11.963 119.894 3100 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.49 % Allowed : 19.37 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.17 (0.17), residues: 2358 helix: 0.50 (0.18), residues: 875 sheet: -0.90 (0.27), residues: 390 loop : -1.80 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 276 TYR 0.012 0.001 TYR B 411 PHE 0.023 0.001 PHE E 321 TRP 0.050 0.002 TRP C 381 HIS 0.004 0.001 HIS H 704 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (19961) covalent geometry : angle 0.68313 / 0.34 (27033) SS BOND : bond 0.00483 / 0.25 ( 1) SS BOND : angle 1.51271 / 0.88 ( 2) hydrogen bonds : bond 0.03802 / 2.58 ( 648) hydrogen bonds : angle 4.83001 / 3.26 ( 1856) metal coordination : bond 0.00624 / 0.26 ( 4) metal coordination : angle 4.89009 / 2.41 ( 6) Misc. bond : bond 0.00095 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 TYR cc_start: 0.8777 (m-10) cc_final: 0.8542 (m-10) REVERT: A 138 SER cc_start: 0.9309 (m) cc_final: 0.8893 (t) REVERT: A 148 ASN cc_start: 0.8526 (p0) cc_final: 0.8148 (m110) REVERT: A 166 MET cc_start: 0.8853 (mmm) cc_final: 0.8604 (mtp) REVERT: A 269 LEU cc_start: 0.8739 (mt) cc_final: 0.8475 (mt) REVERT: A 316 MET cc_start: 0.8642 (mmp) cc_final: 0.8276 (mmm) REVERT: A 379 ASP cc_start: 0.8701 (m-30) cc_final: 0.8123 (t70) REVERT: A 425 HIS cc_start: 0.6636 (t-170) cc_final: 0.6078 (t-90) REVERT: A 468 ASN cc_start: 0.8582 (m-40) cc_final: 0.7897 (t0) REVERT: A 533 MET cc_start: 0.8201 (mmt) cc_final: 0.7942 (mmt) REVERT: B 131 LYS cc_start: 0.8677 (mppt) cc_final: 0.7848 (mppt) REVERT: B 467 LYS cc_start: 0.9133 (pttt) cc_final: 0.8877 (ptpp) REVERT: C 333 MET cc_start: 0.8986 (mpp) cc_final: 0.8023 (mpp) REVERT: C 341 MET cc_start: 0.9314 (mmt) cc_final: 0.8929 (mmp) REVERT: C 344 GLU cc_start: 0.8205 (pm20) cc_final: 0.7896 (pm20) REVERT: C 430 VAL cc_start: 0.9472 (p) cc_final: 0.9134 (p) REVERT: C 438 GLU cc_start: 0.9039 (tp30) cc_final: 0.8757 (tp30) REVERT: C 443 ASP cc_start: 0.8748 (m-30) cc_final: 0.8434 (m-30) REVERT: D 352 ASP cc_start: 0.8783 (t0) cc_final: 0.8349 (t0) REVERT: D 412 MET cc_start: 0.8935 (mmp) cc_final: 0.8717 (mmm) REVERT: D 425 HIS cc_start: 0.8472 (t-90) cc_final: 0.8049 (t-90) REVERT: D 471 LYS cc_start: 0.8451 (tptp) cc_final: 0.8004 (mmmt) REVERT: D 533 MET cc_start: 0.8047 (mpp) cc_final: 0.7767 (mpp) REVERT: E 289 PHE cc_start: 0.8488 (m-80) cc_final: 0.7957 (m-80) REVERT: E 348 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: E 377 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6377 (ptpp) REVERT: E 448 LYS cc_start: 0.9234 (ttmt) cc_final: 0.8974 (mmtm) REVERT: H 182 LEU cc_start: 0.9014 (tt) cc_final: 0.8736 (tt) REVERT: H 217 GLU cc_start: 0.8775 (tp30) cc_final: 0.8394 (tp30) REVERT: H 649 MET cc_start: 0.8598 (mtm) cc_final: 0.7885 (mtm) outliers start: 50 outliers final: 45 residues processed: 255 average time/residue: 0.1284 time to fit residues: 52.2273 Evaluate side-chains 262 residues out of total 2017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 189 CYS Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 546 SER Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 292 CYS Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 518 ILE Chi-restraints excluded: chain E residue 348 GLU Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 391 PHE Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 464 CYS Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 174 ASP Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 265 TYR Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 537 ILE Chi-restraints excluded: chain H residue 555 PHE Chi-restraints excluded: chain H residue 629 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: [40, 232, 70, 222, 8, 61, 116, 191, 164, 228, 31] chunk 40 optimal weight: 0.0770 chunk 232 optimal weight: 0.0470 chunk 70 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.072788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.054958 restraints weight = 83856.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.056688 restraints weight = 44633.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.057837 restraints weight = 29638.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.058560 restraints weight = 22518.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.059062 restraints weight = 18829.476| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19967 Z= 0.138 Angle : 0.673 14.107 27041 Z= 0.335 Chirality : 0.045 0.315 2979 Planarity : 0.004 0.121 3346 Dihedral : 11.879 118.465 3100 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.19 % Allowed : 19.77 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % 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: -1.04 (0.17), residues: 2358 helix: 0.61 (0.18), residues: 874 sheet: -0.83 (0.27), residues: 387 loop : -1.73 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 361 TYR 0.013 0.001 TYR H 203 PHE 0.014 0.001 PHE H 163 TRP 0.047 0.002 TRP C 381 HIS 0.006 0.001 HIS H 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (19961) covalent geometry : angle 0.66978 / 0.33 (27033) SS BOND : bond 0.00139 / 0.07 ( 1) SS BOND : angle 1.55451 / 0.90 ( 2) hydrogen bonds : bond 0.03548 / 2.41 ( 648) hydrogen bonds : angle 4.69008 / 3.16 ( 1856) metal coordination : bond 0.00548 / 0.23 ( 4) metal coordination : angle 4.21913 / 2.06 ( 6) Misc. bond : bond 0.00090 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3797.36 seconds wall clock time: 66 minutes 21.68 seconds (3981.68 seconds total)