Starting phenix.real_space_refine on Tue Sep 15 10:07:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6hts_3954/09_2026/6hts_3954.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hts_3954/09_2026/6hts_3954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6hts_3954/09_2026/6hts_3954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hts_3954/09_2026/6hts_3954.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6hts_3954/09_2026/6hts_3954.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6hts_3954/09_2026/6hts_3954.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hts_3954/09_2026/6hts_3954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hts_3954/09_2026/6hts_3954.map" } resolution = 4.8 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 External origin is not on a grid point...ignoring external origin ***Please contact the Phenix developers if you need Phenix to use this external_origin*** ------------------------------------------------------------------------------- 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 312 5.49 5 S 127 5.16 5 C 23263 2.51 5 N 7024 2.21 5 O 8017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38744 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3344 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 16, 'TRANS': 417} Chain breaks: 1 Chain: "B" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3299 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3358 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 420} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3347 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3403 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 425} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3365 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 4100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 4100 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 404} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 651} Chain breaks: 3 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1548 Unresolved non-hydrogen angles: 1970 Unresolved non-hydrogen dihedrals: 1304 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'PHE:plan': 17, 'ASN:plan1': 20, 'TYR:plan': 16, 'GLN:plan1': 31, 'TRP:plan': 9, 'GLU:plan': 23, 'ASP:plan': 21, 'HIS:plan': 11, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 874 Chain: "H" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 1612 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 284} Link IDs: {'PTRANS': 15, 'TRANS': 310} Chain breaks: 3 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1086 Unresolved non-hydrogen angles: 1397 Unresolved non-hydrogen dihedrals: 920 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'ASP:plan': 14, 'ASN:plan1': 15, 'PHE:plan': 12, 'GLN:plan1': 17, 'ARG:plan': 18, 'TRP:plan': 5, 'GLU:plan': 28, 'TYR:plan': 18, 'HIS:plan': 9} Unresolved non-hydrogen planarities: 645 Chain: "I" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "J" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "K" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "L" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "M" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "N" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "O" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "P" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain breaks: 1 Chain: "R" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 533 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 12, 'TRANS': 59} Chain: "X" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3095 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "Y" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3055 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 32172 SG CYS R 309 15.196 57.020 139.538 1.00491.05 S ATOM 32202 SG CYS R 314 14.803 58.094 142.961 1.00363.48 S ATOM 32327 SG CYS R 330 18.181 58.617 142.084 1.00347.03 S ATOM 32356 SG CYS R 334 16.126 54.758 142.936 1.00472.04 S Time building chain proxies: 9.11, per 1000 atoms: 0.24 Number of scatterers: 38744 At special positions: 0 Unit cell: (141.7, 179.85, 211.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 127 16.00 P 312 15.00 O 8017 8.00 N 7024 7.00 C 23263 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 401 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 334 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 330 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 309 " pdb="ZN ZN R 401 " - pdb=" SG CYS R 314 " Number of angles added : 6 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8278 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 0 sheets defined 51.7% alpha, 0.0% beta 124 base pairs and 246 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.846A pdb=" N LYS A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 removed outlier: 3.607A pdb=" N GLY A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.895A pdb=" N ILE A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 183 Processing helix chain 'A' and resid 208 through 212 removed outlier: 4.178A pdb=" N THR A 211 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 212 " --> pdb=" O TYR A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.781A pdb=" N ARG A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 272 through 290 removed outlier: 3.542A pdb=" N ARG A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN A 284 " --> pdb=" O ASN A 280 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.742A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.784A pdb=" N ARG A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.713A pdb=" N SER A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 421 removed outlier: 3.527A pdb=" N ALA A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.543A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 451 removed outlier: 3.675A pdb=" N ALA A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 66 Processing helix chain 'B' and resid 82 through 95 removed outlier: 4.362A pdb=" N GLY B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.531A pdb=" N ASP B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'B' and resid 255 through 263 Processing helix chain 'B' and resid 269 through 287 removed outlier: 3.650A pdb=" N ARG B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 318 removed outlier: 4.136A pdb=" N ASN B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 346 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 363 through 379 removed outlier: 3.603A pdb=" N LYS B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 398 through 417 removed outlier: 3.729A pdb=" N ALA B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 407 " --> pdb=" O ILE B 403 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 433 Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'C' and resid 42 through 59 removed outlier: 3.975A pdb=" N VAL C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 88 removed outlier: 3.704A pdb=" N GLY C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.731A pdb=" N VAL C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 183 Processing helix chain 'C' and resid 208 through 212 removed outlier: 4.219A pdb=" N THR C 211 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU C 212 " --> pdb=" O TYR C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 212' Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 272 through 290 Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.997A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 350 Processing helix chain 'C' and resid 351 through 358 removed outlier: 3.582A pdb=" N ARG C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 382 removed outlier: 3.798A pdb=" N LYS C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 401 Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.856A pdb=" N SER C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 421 removed outlier: 3.706A pdb=" N ALA C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 437 Processing helix chain 'C' and resid 439 through 450 removed outlier: 3.832A pdb=" N ALA C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP C 449 " --> pdb=" O LYS C 445 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN C 450 " --> pdb=" O ILE C 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 82 through 94 removed outlier: 3.578A pdb=" N ALA D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 127 removed outlier: 3.736A pdb=" N ILE D 127 " --> pdb=" O PHE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 244 through 253 Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.567A pdb=" N LEU D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 287 removed outlier: 3.548A pdb=" N ARG D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.653A pdb=" N MET D 303 " --> pdb=" O GLU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.623A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 346 Processing helix chain 'D' and resid 347 through 354 Processing helix chain 'D' and resid 363 through 379 removed outlier: 3.677A pdb=" N LYS D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG D 374 " --> pdb=" O ILE D 370 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D 376 " --> pdb=" O ARG D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 397 removed outlier: 4.003A pdb=" N VAL D 389 " --> pdb=" O ASP D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 416 Processing helix chain 'D' and resid 422 through 433 removed outlier: 3.514A pdb=" N ILE D 426 " --> pdb=" O GLN D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 446 Processing helix chain 'E' and resid 42 through 59 removed outlier: 3.604A pdb=" N GLU E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 88 removed outlier: 3.786A pdb=" N ALA E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 102 removed outlier: 3.526A pdb=" N TYR E 102 " --> pdb=" O SER E 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 99 through 102' Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.826A pdb=" N ILE E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 183 removed outlier: 3.672A pdb=" N GLU E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER E 179 " --> pdb=" O SER E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 4.185A pdb=" N THR E 211 " --> pdb=" O THR E 208 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU E 212 " --> pdb=" O TYR E 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 208 through 212' Processing helix chain 'E' and resid 240 through 249 Processing helix chain 'E' and resid 255 through 264 Processing helix chain 'E' and resid 272 through 290 removed outlier: 3.722A pdb=" N ARG E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 308 through 320 removed outlier: 3.871A pdb=" N HIS E 316 " --> pdb=" O PHE E 312 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 350 Processing helix chain 'E' and resid 351 through 358 Processing helix chain 'E' and resid 367 through 383 Processing helix chain 'E' and resid 387 through 401 Processing helix chain 'E' and resid 402 through 409 removed outlier: 3.545A pdb=" N SER E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 421 removed outlier: 3.835A pdb=" N ALA E 413 " --> pdb=" O LEU E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 437 Processing helix chain 'E' and resid 439 through 450 removed outlier: 3.636A pdb=" N ALA E 448 " --> pdb=" O ALA E 444 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP E 449 " --> pdb=" O LYS E 445 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN E 450 " --> pdb=" O ILE E 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.820A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 126 removed outlier: 4.025A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 185 removed outlier: 3.566A pdb=" N LEU F 182 " --> pdb=" O MET F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 213 Processing helix chain 'F' and resid 244 through 253 removed outlier: 3.839A pdb=" N ASP F 248 " --> pdb=" O LEU F 244 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL F 249 " --> pdb=" O HIS F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 263 removed outlier: 4.252A pdb=" N ALA F 259 " --> pdb=" O GLN F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 287 removed outlier: 3.758A pdb=" N ARG F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 318 removed outlier: 4.047A pdb=" N ASN F 313 " --> pdb=" O PHE F 309 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 346 Processing helix chain 'F' and resid 347 through 352 removed outlier: 3.684A pdb=" N ASP F 352 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 379 removed outlier: 3.738A pdb=" N LYS F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN F 369 " --> pdb=" O LYS F 365 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU F 377 " --> pdb=" O ILE F 373 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 397 removed outlier: 3.950A pdb=" N VAL F 389 " --> pdb=" O ASP F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.801A pdb=" N ALA F 402 " --> pdb=" O SER F 398 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU F 411 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 removed outlier: 3.647A pdb=" N ILE F 426 " --> pdb=" O GLN F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'G' and resid 519 through 535 removed outlier: 3.781A pdb=" N GLN G 535 " --> pdb=" O ASN G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 547 Processing helix chain 'G' and resid 548 through 558 Processing helix chain 'G' and resid 578 through 590 Processing helix chain 'G' and resid 601 through 613 Processing helix chain 'G' and resid 630 through 637 Processing helix chain 'G' and resid 637 through 642 Processing helix chain 'G' and resid 654 through 658 Processing helix chain 'G' and resid 662 through 671 removed outlier: 3.727A pdb=" N LYS G 666 " --> pdb=" O SER G 662 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE G 671 " --> pdb=" O ILE G 667 " (cutoff:3.500A) Processing helix chain 'G' and resid 687 through 699 removed outlier: 3.826A pdb=" N LEU G 691 " --> pdb=" O THR G 687 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE G 698 " --> pdb=" O LEU G 694 " (cutoff:3.500A) Processing helix chain 'G' and resid 727 through 740 removed outlier: 3.549A pdb=" N MET G 737 " --> pdb=" O SER G 733 " (cutoff:3.500A) Processing helix chain 'G' and resid 768 through 779 removed outlier: 3.953A pdb=" N LYS G 779 " --> pdb=" O TYR G 775 " (cutoff:3.500A) Processing helix chain 'G' and resid 809 through 816 removed outlier: 3.685A pdb=" N ARG G 813 " --> pdb=" O VAL G 809 " (cutoff:3.500A) Processing helix chain 'G' and resid 841 through 847 Processing helix chain 'G' and resid 854 through 864 Processing helix chain 'G' and resid 868 through 878 Processing helix chain 'G' and resid 888 through 894 removed outlier: 3.564A pdb=" N ARG G 892 " --> pdb=" O PHE G 888 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE G 893 " --> pdb=" O SER G 889 " (cutoff:3.500A) Processing helix chain 'G' and resid 897 through 908 removed outlier: 3.751A pdb=" N GLY G 908 " --> pdb=" O LEU G 904 " (cutoff:3.500A) Processing helix chain 'G' and resid 908 through 931 removed outlier: 3.886A pdb=" N ARG G 912 " --> pdb=" O GLY G 908 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS G 921 " --> pdb=" O PHE G 917 " (cutoff:3.500A) Processing helix chain 'G' and resid 937 through 942 Processing helix chain 'G' and resid 958 through 965 removed outlier: 3.518A pdb=" N CYS G 965 " --> pdb=" O ASN G 961 " (cutoff:3.500A) Processing helix chain 'G' and resid 965 through 972 removed outlier: 3.739A pdb=" N VAL G 972 " --> pdb=" O LEU G 968 " (cutoff:3.500A) Processing helix chain 'G' and resid 1029 through 1040 Processing helix chain 'G' and resid 1043 through 1052 Processing helix chain 'G' and resid 1054 through 1065 Processing helix chain 'G' and resid 1100 through 1117 removed outlier: 3.576A pdb=" N TYR G1104 " --> pdb=" O SER G1100 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER G1115 " --> pdb=" O THR G1111 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN G1116 " --> pdb=" O ARG G1112 " (cutoff:3.500A) Processing helix chain 'G' and resid 1126 through 1139 removed outlier: 3.832A pdb=" N TYR G1139 " --> pdb=" O GLU G1135 " (cutoff:3.500A) Processing helix chain 'G' and resid 1152 through 1162 Processing helix chain 'G' and resid 1175 through 1180 Processing helix chain 'G' and resid 1201 through 1209 removed outlier: 3.828A pdb=" N ARG G1209 " --> pdb=" O GLN G1205 " (cutoff:3.500A) Processing helix chain 'G' and resid 1230 through 1248 removed outlier: 4.004A pdb=" N ILE G1234 " --> pdb=" O ILE G1230 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 121 Processing helix chain 'H' and resid 141 through 155 Processing helix chain 'H' and resid 165 through 175 Processing helix chain 'H' and resid 214 through 230 removed outlier: 3.777A pdb=" N TYR H 230 " --> pdb=" O LEU H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 237 removed outlier: 3.620A pdb=" N LEU H 234 " --> pdb=" O TYR H 230 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA H 235 " --> pdb=" O PRO H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 250 removed outlier: 3.562A pdb=" N SER H 250 " --> pdb=" O LEU H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 264 Processing helix chain 'H' and resid 446 through 451 Processing helix chain 'H' and resid 452 through 455 Processing helix chain 'H' and resid 457 through 461 removed outlier: 3.557A pdb=" N LEU H 460 " --> pdb=" O GLN H 457 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE H 461 " --> pdb=" O PRO H 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 457 through 461' Processing helix chain 'H' and resid 467 through 479 removed outlier: 3.850A pdb=" N ARG H 478 " --> pdb=" O TYR H 474 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR H 479 " --> pdb=" O ILE H 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 482 through 490 removed outlier: 4.418A pdb=" N MET H 486 " --> pdb=" O ASP H 482 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 500 removed outlier: 4.282A pdb=" N TYR H 500 " --> pdb=" O ASN H 497 " (cutoff:3.500A) Processing helix chain 'H' and resid 502 through 515 Processing helix chain 'H' and resid 531 through 543 Processing helix chain 'H' and resid 543 through 551 Processing helix chain 'H' and resid 553 through 561 Processing helix chain 'H' and resid 562 through 567 Processing helix chain 'I' and resid 44 through 57 Processing helix chain 'I' and resid 63 through 79 removed outlier: 3.663A pdb=" N ASP I 77 " --> pdb=" O GLU I 73 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE I 78 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 114 Processing helix chain 'I' and resid 120 through 132 Processing helix chain 'J' and resid 30 through 41 Processing helix chain 'J' and resid 49 through 76 removed outlier: 3.756A pdb=" N GLU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG J 67 " --> pdb=" O GLU J 63 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP J 68 " --> pdb=" O ASN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 93 removed outlier: 3.758A pdb=" N VAL J 86 " --> pdb=" O THR J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 21 Processing helix chain 'K' and resid 26 through 37 removed outlier: 3.957A pdb=" N VAL K 30 " --> pdb=" O PRO K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 73 Processing helix chain 'K' and resid 79 through 90 Processing helix chain 'K' and resid 90 through 97 Processing helix chain 'K' and resid 112 through 116 Processing helix chain 'L' and resid 36 through 49 removed outlier: 4.305A pdb=" N TYR L 40 " --> pdb=" O SER L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 85 removed outlier: 3.723A pdb=" N ASN L 84 " --> pdb=" O LEU L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 102 Processing helix chain 'L' and resid 103 through 124 Processing helix chain 'M' and resid 44 through 57 Processing helix chain 'M' and resid 63 through 79 removed outlier: 3.510A pdb=" N PHE M 67 " --> pdb=" O ARG M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 114 Processing helix chain 'M' and resid 120 through 132 Processing helix chain 'N' and resid 25 through 29 Processing helix chain 'N' and resid 30 through 41 Processing helix chain 'N' and resid 49 through 76 removed outlier: 3.688A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG N 67 " --> pdb=" O GLU N 63 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP N 68 " --> pdb=" O ASN N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 93 removed outlier: 3.813A pdb=" N VAL N 86 " --> pdb=" O THR N 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 21 Processing helix chain 'O' and resid 26 through 37 removed outlier: 3.956A pdb=" N VAL O 30 " --> pdb=" O PRO O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 73 Processing helix chain 'O' and resid 79 through 90 Processing helix chain 'O' and resid 90 through 97 Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'P' and resid 37 through 49 Processing helix chain 'P' and resid 55 through 85 removed outlier: 3.723A pdb=" N ASN P 84 " --> pdb=" O LEU P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 102 Processing helix chain 'P' and resid 103 through 124 Processing helix chain 'R' and resid 331 through 342 removed outlier: 3.599A pdb=" N ILE R 337 " --> pdb=" O GLN R 333 " (cutoff:3.500A) 1431 hydrogen bonds defined for protein. 4215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 313 hydrogen bonds 626 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 246 stacking parallelities Total time for adding SS restraints: 8.69 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11164 1.34 - 1.45: 6803 1.45 - 1.57: 21107 1.57 - 1.69: 618 1.69 - 1.81: 209 Bond restraints: 39901 Sorted by residual: bond pdb=" C SER P 36 " pdb=" N TYR P 37 " ideal model delta sigma weight residual 1.333 1.581 -0.247 1.56e-02 4.11e+03 2.51e+02 bond pdb=" C SER L 36 " pdb=" N TYR L 37 " ideal model delta sigma weight residual 1.333 1.581 -0.247 1.56e-02 4.11e+03 2.51e+02 bond pdb=" C THR G 682 " pdb=" N PRO G 683 " ideal model delta sigma weight residual 1.334 1.428 -0.094 2.34e-02 1.83e+03 1.62e+01 bond pdb=" C1' DA Y 29 " pdb=" N9 DA Y 29 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" C1' DT Y 82 " pdb=" N1 DT Y 82 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.52e+01 ... (remaining 39896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 53973 1.72 - 3.43: 1178 3.43 - 5.15: 131 5.15 - 6.86: 33 6.86 - 8.58: 1 Bond angle restraints: 55316 Sorted by residual: angle pdb=" O4' DA X 16 " pdb=" C1' DA X 16 " pdb=" N9 DA X 16 " ideal model delta sigma weight residual 108.00 111.35 -3.35 7.00e-01 2.04e+00 2.29e+01 angle pdb=" O4' DA X 26 " pdb=" C4' DA X 26 " pdb=" C3' DA X 26 " ideal model delta sigma weight residual 106.00 103.31 2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT X -61 " pdb=" C4 DT X -61 " pdb=" O4 DT X -61 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT X -39 " pdb=" C4 DT X -39 " pdb=" O4 DT X -39 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT Y -17 " pdb=" C4 DT Y -17 " pdb=" O4 DT Y -17 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 ... (remaining 55311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.14: 21328 25.14 - 50.28: 1619 50.28 - 75.42: 506 75.42 - 100.56: 15 100.56 - 125.70: 4 Dihedral angle restraints: 23472 sinusoidal: 10671 harmonic: 12801 Sorted by residual: dihedral pdb=" CA CYS R 314 " pdb=" C CYS R 314 " pdb=" N PRO R 315 " pdb=" CA PRO R 315 " ideal model delta harmonic sigma weight residual -180.00 -135.36 -44.64 0 5.00e+00 4.00e-02 7.97e+01 dihedral pdb=" CA GLY I 44 " pdb=" C GLY I 44 " pdb=" N THR I 45 " pdb=" CA THR I 45 " ideal model delta harmonic sigma weight residual 180.00 141.99 38.01 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" O2A ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PA ADP A 501 " pdb=" PB ADP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 65.70 -125.70 1 2.00e+01 2.50e-03 3.80e+01 ... (remaining 23469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 4037 0.028 - 0.056: 1536 0.056 - 0.084: 483 0.084 - 0.112: 346 0.112 - 0.141: 85 Chirality restraints: 6487 Sorted by residual: chirality pdb=" CA CYS R 314 " pdb=" N CYS R 314 " pdb=" C CYS R 314 " pdb=" CB CYS R 314 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CA PRO R 315 " pdb=" N PRO R 315 " pdb=" C PRO R 315 " pdb=" CB PRO R 315 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE G1090 " pdb=" N ILE G1090 " pdb=" C ILE G1090 " pdb=" CB ILE G1090 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 6484 not shown) Planarity restraints: 6100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS R 314 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO R 315 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO R 315 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 315 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G1071 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO G1072 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO G1072 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G1072 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO B 99 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.024 5.00e-02 4.00e+02 ... (remaining 6097 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 131 2.44 - 3.05: 23328 3.05 - 3.67: 59348 3.67 - 4.28: 88117 4.28 - 4.90: 137002 Nonbonded interactions: 307926 Sorted by model distance: nonbonded pdb=" N2 DG X -45 " pdb=" C2 DA Y 46 " model vdw 1.820 3.420 nonbonded pdb=" C2 DG X 2 " pdb=" N2 DG Y -1 " model vdw 1.975 3.340 nonbonded pdb=" C2 DG X -51 " pdb=" N2 DG Y 52 " model vdw 2.005 3.340 nonbonded pdb=" C2 DG X 38 " pdb=" N2 DG Y -37 " model vdw 2.084 3.340 nonbonded pdb=" C2' DC Y 37 " pdb=" C7 DT Y 38 " model vdw 2.095 3.860 ... (remaining 307921 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 12 through 141 or (resid 152 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 501)) selection = (chain 'C' and (resid 12 through 141 or resid 152 through 501)) selection = (chain 'E' and (resid 12 through 141 or (resid 152 through 153 and (name N or na \ me CA or name C or name O or name CB )) or resid 154 through 501)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 15 through 148 or (resid 149 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 156 through 157 and (name N or name CA or \ name C or name O or name CB )) or resid 158 through 214 or resid 219 through 501 \ )) selection = (chain 'F' and (resid 15 through 149 or resid 156 through 210 or (resid 211 thro \ ugh 214 and (name N or name CA or name C or name O or name CB )) or resid 219 or \ (resid 220 through 223 and (name N or name CA or name C or name O or name CB )) \ or resid 224 through 501)) } ncs_group { reference = chain 'I' selection = (chain 'M' and resid 40 through 135) } ncs_group { reference = chain 'J' selection = (chain 'N' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = (chain 'K' and resid 14 through 118) selection = chain 'O' } ncs_group { reference = (chain 'L' and resid 31 through 124) selection = chain 'P' } 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=0.01 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: 1.360 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: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 43.530 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 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 : 0.004 0.247 39905 Z= 0.334 Angle : 0.612 19.500 55322 Z= 0.418 Chirality : 0.040 0.141 6487 Planarity : 0.003 0.052 6100 Dihedral : 17.812 125.696 15194 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.71 % Favored : 98.27 % Rotamer: Outliers : 1.39 % Allowed : 3.47 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.02 % 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: -2.23 (0.10), residues: 4393 helix: -2.10 (0.08), residues: 2121 sheet: -0.11 (0.17), residues: 608 loop : -0.83 (0.12), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 859 TYR 0.008 0.001 TYR B 442 PHE 0.010 0.001 PHE N 100 TRP 0.005 0.001 TRP G 913 HIS 0.002 0.000 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.33 (39901) covalent geometry : angle 0.59082 / 0.42 (55316) hydrogen bonds : bond 0.09348 / 6.64 ( 1744) hydrogen bonds : angle 7.85960 / 5.49 ( 4841) metal coordination : bond 0.16103 / 7.65 ( 4) metal coordination : angle 15.36505 / 8.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 753 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 42 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8333 (mt0) REVERT: A 278 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8710 (tm-30) REVERT: A 306 MET cc_start: 0.8130 (mtp) cc_final: 0.7895 (ttm) REVERT: A 359 MET cc_start: 0.9099 (mtm) cc_final: 0.8844 (mmt) REVERT: A 441 LYS cc_start: 0.9494 (mttt) cc_final: 0.9210 (mmmt) REVERT: B 73 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.9023 (p) REVERT: B 251 ASN cc_start: 0.7262 (m-40) cc_final: 0.6556 (m-40) REVERT: B 305 ASP cc_start: 0.9126 (t0) cc_final: 0.8849 (p0) REVERT: B 356 ILE cc_start: 0.9527 (mt) cc_final: 0.9243 (mm) REVERT: C 61 MET cc_start: 0.8309 (mmt) cc_final: 0.7976 (tpp) REVERT: C 264 MET cc_start: 0.8851 (mmm) cc_final: 0.8557 (mmm) REVERT: C 306 MET cc_start: 0.9565 (tpp) cc_final: 0.9252 (tpp) REVERT: C 313 THR cc_start: 0.9650 (m) cc_final: 0.9405 (m) REVERT: C 354 LEU cc_start: 0.9662 (tp) cc_final: 0.9436 (mt) REVERT: D 26 SER cc_start: 0.9381 (t) cc_final: 0.9126 (p) REVERT: D 123 PHE cc_start: 0.9258 (m-10) cc_final: 0.9035 (m-80) REVERT: D 185 ASP cc_start: 0.8510 (m-30) cc_final: 0.8190 (m-30) REVERT: D 193 ILE cc_start: 0.9522 (pt) cc_final: 0.9138 (mm) REVERT: D 308 SER cc_start: 0.9161 (m) cc_final: 0.8959 (p) REVERT: E 49 CYS cc_start: 0.9675 (m) cc_final: 0.9406 (p) REVERT: E 191 ILE cc_start: 0.9214 (pt) cc_final: 0.8967 (pt) REVERT: F 46 MET cc_start: 0.8139 (mmm) cc_final: 0.7772 (mpp) REVERT: F 239 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8378 (p) REVERT: F 246 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9120 (mm-30) REVERT: F 443 MET cc_start: 0.8626 (ttp) cc_final: 0.8023 (tpt) REVERT: G 888 PHE cc_start: 0.8980 (m-80) cc_final: 0.8733 (m-10) REVERT: G 905 MET cc_start: 0.8020 (tpp) cc_final: 0.7664 (tpp) REVERT: G 971 LEU cc_start: 0.9483 (tp) cc_final: 0.9231 (mt) REVERT: G 1038 LEU cc_start: 0.9034 (mt) cc_final: 0.8770 (pp) REVERT: K 24 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7751 (tm-30) REVERT: K 49 VAL cc_start: 0.5978 (t) cc_final: 0.5657 (t) REVERT: K 99 ARG cc_start: 0.7343 (mmt180) cc_final: 0.6420 (mpt180) REVERT: L 61 ILE cc_start: 0.8284 (mt) cc_final: 0.7756 (mt) REVERT: L 106 LEU cc_start: 0.7585 (mt) cc_final: 0.7227 (mt) REVERT: M 59 GLU cc_start: 0.4997 (OUTLIER) cc_final: 0.4541 (pm20) REVERT: M 67 PHE cc_start: 0.6390 (t80) cc_final: 0.6141 (t80) REVERT: P 98 VAL cc_start: 0.8536 (t) cc_final: 0.8018 (t) outliers start: 43 outliers final: 8 residues processed: 789 average time/residue: 0.2768 time to fit residues: 344.9937 Evaluate side-chains 442 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 430 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 50.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN A 429 HIS ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 240 HIS B 302 HIS C 34 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 HIS C 380 GLN C 393 HIS C 414 ASN D 255 GLN E 42 GLN E 115 ASN E 203 GLN E 229 HIS F 25 HIS F 146 GLN F 240 HIS F 245 HIS F 302 HIS F 344 HIS F 404 GLN G 855 HIS ** G 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN L 47 GLN L 82 HIS ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN ** L 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 HIS ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 GLN O 112 GLN P 49 HIS ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.080295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.059612 restraints weight = 373955.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.060729 restraints weight = 261188.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.061483 restraints weight = 197447.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.062177 restraints weight = 158808.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.062629 restraints weight = 133474.707| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 39905 Z= 0.173 Angle : 0.639 14.732 55322 Z= 0.337 Chirality : 0.043 0.254 6487 Planarity : 0.005 0.109 6100 Dihedral : 22.401 124.310 8099 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.12 % Favored : 98.86 % Rotamer: Outliers : 0.10 % Allowed : 2.40 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.11), residues: 4393 helix: -0.25 (0.10), residues: 2172 sheet: 0.30 (0.17), residues: 622 loop : -0.49 (0.13), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 99 TYR 0.038 0.002 TYR P 37 PHE 0.034 0.002 PHE G 949 TRP 0.009 0.001 TRP D 283 HIS 0.014 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (39901) covalent geometry : angle 0.63331 / 0.34 (55316) hydrogen bonds : bond 0.04781 / 3.20 ( 1744) hydrogen bonds : angle 4.73393 / 3.28 ( 4841) metal coordination : bond 0.01326 / 0.61 ( 4) metal coordination : angle 7.89841 / 4.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 482 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8292 (tm-30) REVERT: A 306 MET cc_start: 0.8659 (mtp) cc_final: 0.8239 (ttm) REVERT: A 329 PHE cc_start: 0.9372 (m-80) cc_final: 0.9073 (m-80) REVERT: A 359 MET cc_start: 0.8215 (mtm) cc_final: 0.8006 (mmt) REVERT: A 371 MET cc_start: 0.9520 (mpp) cc_final: 0.9017 (mpp) REVERT: B 305 ASP cc_start: 0.9114 (t0) cc_final: 0.8397 (p0) REVERT: C 57 LYS cc_start: 0.9141 (mtmm) cc_final: 0.8868 (ptpp) REVERT: C 108 LYS cc_start: 0.8789 (mtpt) cc_final: 0.8249 (mmmm) REVERT: C 259 MET cc_start: 0.9369 (mmm) cc_final: 0.9074 (mmm) REVERT: C 260 MET cc_start: 0.9065 (tpt) cc_final: 0.7947 (tpt) REVERT: C 263 LEU cc_start: 0.9150 (mm) cc_final: 0.8851 (mm) REVERT: C 264 MET cc_start: 0.9080 (mmm) cc_final: 0.7950 (mmm) REVERT: C 286 TYR cc_start: 0.9078 (m-80) cc_final: 0.7963 (m-80) REVERT: C 306 MET cc_start: 0.9134 (tpp) cc_final: 0.8599 (tpp) REVERT: C 312 PHE cc_start: 0.9408 (m-10) cc_final: 0.9179 (m-10) REVERT: C 313 THR cc_start: 0.9441 (m) cc_final: 0.9201 (m) REVERT: C 316 HIS cc_start: 0.8900 (m-70) cc_final: 0.8274 (m90) REVERT: C 320 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7805 (mm-30) REVERT: C 371 MET cc_start: 0.8804 (mtm) cc_final: 0.8365 (mtp) REVERT: D 113 MET cc_start: 0.7903 (ptm) cc_final: 0.7523 (ppp) REVERT: D 178 MET cc_start: 0.9393 (mmp) cc_final: 0.9121 (mmm) REVERT: D 193 ILE cc_start: 0.9396 (pt) cc_final: 0.9030 (mm) REVERT: D 274 GLU cc_start: 0.9472 (tm-30) cc_final: 0.9181 (tm-30) REVERT: D 308 SER cc_start: 0.9571 (m) cc_final: 0.9089 (t) REVERT: D 382 MET cc_start: 0.9080 (tpt) cc_final: 0.8363 (tpp) REVERT: D 443 MET cc_start: 0.8864 (ptm) cc_final: 0.8088 (ptm) REVERT: E 113 MET cc_start: 0.9517 (tpp) cc_final: 0.9057 (tpp) REVERT: E 147 MET cc_start: 0.3112 (ptp) cc_final: 0.2831 (pmm) REVERT: E 182 LYS cc_start: 0.9675 (ptmm) cc_final: 0.9330 (ptpt) REVERT: E 371 MET cc_start: 0.9333 (mtp) cc_final: 0.8674 (mtp) REVERT: F 62 MET cc_start: 0.9197 (ttm) cc_final: 0.8920 (mtt) REVERT: F 246 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8779 (mt-10) REVERT: F 443 MET cc_start: 0.7878 (ttp) cc_final: 0.7139 (tpt) REVERT: G 827 THR cc_start: 0.9008 (p) cc_final: 0.8737 (t) REVERT: G 895 ASP cc_start: 0.9017 (p0) cc_final: 0.8754 (p0) REVERT: G 896 ILE cc_start: 0.9294 (mm) cc_final: 0.8780 (mm) REVERT: G 917 PHE cc_start: 0.9588 (t80) cc_final: 0.9259 (t80) REVERT: G 929 LEU cc_start: 0.9559 (tp) cc_final: 0.9294 (mm) REVERT: G 1023 ASP cc_start: 0.8947 (p0) cc_final: 0.8744 (t0) REVERT: K 24 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8049 (tm-30) REVERT: K 99 ARG cc_start: 0.7321 (mmt180) cc_final: 0.6326 (mpt180) REVERT: P 45 LEU cc_start: 0.4299 (tt) cc_final: 0.4014 (tt) REVERT: P 80 LEU cc_start: 0.7391 (mt) cc_final: 0.6550 (mt) outliers start: 3 outliers final: 0 residues processed: 485 average time/residue: 0.2590 time to fit residues: 200.2423 Evaluate side-chains 337 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 306 optimal weight: 0.0470 chunk 455 optimal weight: 50.0000 chunk 424 optimal weight: 30.0000 chunk 81 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 401 optimal weight: 4.9990 chunk 428 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 67.6772 > 50:) chunk 242 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN B 329 ASN C 42 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 HIS F 78 GLN F 344 HIS G 873 GLN ** G 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 ASN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.078622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.058170 restraints weight = 379312.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.059190 restraints weight = 269057.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.060001 restraints weight = 199990.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.060775 restraints weight = 155663.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.061175 restraints weight = 128313.013| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39905 Z= 0.153 Angle : 0.596 15.104 55322 Z= 0.317 Chirality : 0.041 0.210 6487 Planarity : 0.005 0.105 6100 Dihedral : 22.533 124.374 8099 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.48 % Favored : 98.50 % Rotamer: Outliers : 0.10 % Allowed : 2.30 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.12), residues: 4393 helix: 0.52 (0.11), residues: 2164 sheet: 0.53 (0.18), residues: 630 loop : -0.23 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 14 TYR 0.036 0.002 TYR I 99 PHE 0.024 0.002 PHE A 177 TRP 0.023 0.002 TRP G1077 HIS 0.013 0.001 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (39901) covalent geometry : angle 0.59146 / 0.32 (55316) hydrogen bonds : bond 0.04339 / 2.90 ( 1744) hydrogen bonds : angle 4.33213 / 3.01 ( 4841) metal coordination : bond 0.00940 / 0.42 ( 4) metal coordination : angle 6.86216 / 3.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 410 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 113 MET cc_start: 0.9151 (ttp) cc_final: 0.8900 (ptm) REVERT: A 259 MET cc_start: 0.9678 (tpp) cc_final: 0.9370 (tpp) REVERT: A 278 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8291 (tm-30) REVERT: A 306 MET cc_start: 0.8653 (mtp) cc_final: 0.8226 (ttm) REVERT: A 329 PHE cc_start: 0.9339 (m-80) cc_final: 0.9095 (m-80) REVERT: A 359 MET cc_start: 0.8356 (mtm) cc_final: 0.8008 (mmt) REVERT: B 20 GLU cc_start: 0.9513 (mm-30) cc_final: 0.9280 (mm-30) REVERT: B 305 ASP cc_start: 0.9081 (t0) cc_final: 0.8522 (p0) REVERT: C 191 ILE cc_start: 0.9201 (pt) cc_final: 0.8795 (mp) REVERT: C 259 MET cc_start: 0.9366 (mmm) cc_final: 0.9047 (mmm) REVERT: C 260 MET cc_start: 0.9141 (tpt) cc_final: 0.8185 (tpt) REVERT: C 263 LEU cc_start: 0.9232 (mm) cc_final: 0.8978 (mm) REVERT: C 264 MET cc_start: 0.9155 (mmm) cc_final: 0.8104 (mmm) REVERT: C 306 MET cc_start: 0.9102 (tpp) cc_final: 0.8614 (tpp) REVERT: C 312 PHE cc_start: 0.9461 (m-10) cc_final: 0.9194 (m-80) REVERT: C 320 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7992 (mm-30) REVERT: C 371 MET cc_start: 0.8848 (mtm) cc_final: 0.8616 (mpp) REVERT: D 73 VAL cc_start: 0.9217 (t) cc_final: 0.8975 (p) REVERT: D 113 MET cc_start: 0.8081 (ptm) cc_final: 0.7625 (ppp) REVERT: D 119 LEU cc_start: 0.9658 (mt) cc_final: 0.9192 (mt) REVERT: D 123 PHE cc_start: 0.9423 (m-10) cc_final: 0.8902 (m-80) REVERT: D 193 ILE cc_start: 0.9403 (pt) cc_final: 0.9035 (mm) REVERT: D 274 GLU cc_start: 0.9503 (tm-30) cc_final: 0.9229 (tm-30) REVERT: D 308 SER cc_start: 0.9567 (m) cc_final: 0.8967 (t) REVERT: D 320 MET cc_start: 0.8620 (mmp) cc_final: 0.8415 (mmm) REVERT: D 382 MET cc_start: 0.9269 (tpt) cc_final: 0.8392 (tpp) REVERT: D 443 MET cc_start: 0.8890 (ptm) cc_final: 0.8095 (ptm) REVERT: E 96 MET cc_start: 0.8941 (tmm) cc_final: 0.8738 (tmm) REVERT: E 113 MET cc_start: 0.9520 (tpp) cc_final: 0.9053 (tpp) REVERT: E 182 LYS cc_start: 0.9641 (ptmm) cc_final: 0.9418 (ptpp) REVERT: E 364 MET cc_start: 0.9289 (pmm) cc_final: 0.9022 (pmm) REVERT: E 371 MET cc_start: 0.9338 (mtp) cc_final: 0.8444 (mpp) REVERT: F 174 LEU cc_start: 0.8131 (pt) cc_final: 0.7757 (pt) REVERT: F 218 MET cc_start: 0.8041 (tpp) cc_final: 0.7493 (tpp) REVERT: F 382 MET cc_start: 0.7886 (mmp) cc_final: 0.7291 (mmt) REVERT: F 443 MET cc_start: 0.7942 (ttp) cc_final: 0.7193 (tpt) REVERT: G 901 MET cc_start: 0.9164 (tmm) cc_final: 0.8926 (tmm) REVERT: G 1023 ASP cc_start: 0.9046 (p0) cc_final: 0.8782 (t0) REVERT: K 24 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8014 (tm-30) REVERT: K 99 ARG cc_start: 0.7209 (mmt180) cc_final: 0.6115 (mpt180) REVERT: P 80 LEU cc_start: 0.7271 (mt) cc_final: 0.6681 (mt) outliers start: 3 outliers final: 0 residues processed: 413 average time/residue: 0.2469 time to fit residues: 165.1569 Evaluate side-chains 312 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 121 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 311 optimal weight: 1.9990 chunk 287 optimal weight: 0.7980 chunk 342 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 369 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN D 245 HIS E 203 GLN F 146 GLN F 221 GLN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.077943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.057557 restraints weight = 378337.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.058569 restraints weight = 263385.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.059326 restraints weight = 195283.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.060074 restraints weight = 154445.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.060592 restraints weight = 126911.315| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 39905 Z= 0.133 Angle : 0.568 13.361 55322 Z= 0.301 Chirality : 0.040 0.205 6487 Planarity : 0.004 0.088 6100 Dihedral : 22.531 126.768 8099 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.66 % Favored : 98.32 % Rotamer: Outliers : 0.03 % Allowed : 1.85 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.12), residues: 4393 helix: 0.87 (0.11), residues: 2168 sheet: 0.60 (0.18), residues: 617 loop : -0.10 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.035 0.001 TYR P 83 PHE 0.028 0.001 PHE I 104 TRP 0.065 0.002 TRP F 283 HIS 0.008 0.001 HIS L 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (39901) covalent geometry : angle 0.56376 / 0.30 (55316) hydrogen bonds : bond 0.04036 / 2.70 ( 1744) hydrogen bonds : angle 4.07978 / 2.84 ( 4841) metal coordination : bond 0.00930 / 0.41 ( 4) metal coordination : angle 6.56458 / 3.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 113 MET cc_start: 0.9066 (ttp) cc_final: 0.8716 (ptm) REVERT: A 259 MET cc_start: 0.9629 (tpp) cc_final: 0.9348 (tpp) REVERT: A 278 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8708 (mm-30) REVERT: A 306 MET cc_start: 0.8553 (mtp) cc_final: 0.8127 (ttm) REVERT: A 329 PHE cc_start: 0.9392 (m-80) cc_final: 0.8999 (m-80) REVERT: A 359 MET cc_start: 0.8327 (mtm) cc_final: 0.7924 (mmt) REVERT: B 20 GLU cc_start: 0.9509 (mm-30) cc_final: 0.9226 (mm-30) REVERT: C 191 ILE cc_start: 0.9196 (pt) cc_final: 0.8790 (mp) REVERT: C 259 MET cc_start: 0.9411 (mmm) cc_final: 0.9108 (mmm) REVERT: C 260 MET cc_start: 0.9155 (tpt) cc_final: 0.8157 (tpt) REVERT: C 263 LEU cc_start: 0.9292 (mm) cc_final: 0.9038 (mm) REVERT: C 264 MET cc_start: 0.9221 (mmm) cc_final: 0.8128 (mmm) REVERT: C 306 MET cc_start: 0.9029 (tpp) cc_final: 0.8826 (tpp) REVERT: C 312 PHE cc_start: 0.9447 (m-10) cc_final: 0.9210 (m-80) REVERT: C 313 THR cc_start: 0.9434 (m) cc_final: 0.9010 (m) REVERT: C 316 HIS cc_start: 0.8828 (m90) cc_final: 0.8305 (m90) REVERT: C 332 ASN cc_start: 0.9223 (p0) cc_final: 0.8918 (p0) REVERT: C 371 MET cc_start: 0.8909 (mtm) cc_final: 0.8652 (mpp) REVERT: D 46 MET cc_start: 0.8816 (tpt) cc_final: 0.8186 (tpt) REVERT: D 73 VAL cc_start: 0.9243 (t) cc_final: 0.8985 (p) REVERT: D 178 MET cc_start: 0.9415 (mmp) cc_final: 0.9080 (mmm) REVERT: D 193 ILE cc_start: 0.9424 (pt) cc_final: 0.9209 (mp) REVERT: D 274 GLU cc_start: 0.9470 (tm-30) cc_final: 0.9204 (tm-30) REVERT: D 308 SER cc_start: 0.9552 (m) cc_final: 0.9236 (p) REVERT: D 320 MET cc_start: 0.8707 (mmp) cc_final: 0.8431 (mmm) REVERT: D 382 MET cc_start: 0.9333 (tpt) cc_final: 0.8471 (tpp) REVERT: D 443 MET cc_start: 0.8885 (ptm) cc_final: 0.8008 (ptm) REVERT: E 96 MET cc_start: 0.8826 (tmm) cc_final: 0.8598 (tmm) REVERT: E 113 MET cc_start: 0.9515 (tpp) cc_final: 0.9048 (tpp) REVERT: E 182 LYS cc_start: 0.9619 (ptmm) cc_final: 0.9314 (ptpt) REVERT: E 191 ILE cc_start: 0.9353 (pt) cc_final: 0.8901 (pt) REVERT: E 260 MET cc_start: 0.9560 (tmm) cc_final: 0.9279 (tmm) REVERT: E 264 MET cc_start: 0.8123 (mmp) cc_final: 0.7894 (mmt) REVERT: E 364 MET cc_start: 0.9243 (pmm) cc_final: 0.8993 (pmm) REVERT: E 371 MET cc_start: 0.9346 (mtp) cc_final: 0.8644 (mtp) REVERT: F 90 MET cc_start: 0.9213 (ttt) cc_final: 0.8722 (tpt) REVERT: F 174 LEU cc_start: 0.8502 (pt) cc_final: 0.8086 (pt) REVERT: F 185 ASP cc_start: 0.9173 (m-30) cc_final: 0.8865 (m-30) REVERT: F 218 MET cc_start: 0.8049 (tpp) cc_final: 0.7565 (tpp) REVERT: F 382 MET cc_start: 0.7762 (mmp) cc_final: 0.7237 (mmp) REVERT: F 443 MET cc_start: 0.7932 (ttp) cc_final: 0.7200 (tpt) REVERT: G 901 MET cc_start: 0.9164 (tmm) cc_final: 0.8900 (tmm) REVERT: G 1023 ASP cc_start: 0.8986 (p0) cc_final: 0.8716 (t0) REVERT: K 24 GLN cc_start: 0.8432 (mm-40) cc_final: 0.7981 (tm-30) REVERT: K 99 ARG cc_start: 0.7245 (mmt180) cc_final: 0.6191 (mpt180) REVERT: P 80 LEU cc_start: 0.7511 (mt) cc_final: 0.7309 (mt) outliers start: 1 outliers final: 0 residues processed: 378 average time/residue: 0.2415 time to fit residues: 151.1700 Evaluate side-chains 304 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 91 optimal weight: 4.9990 chunk 464 optimal weight: 50.0000 chunk 150 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 280 optimal weight: 8.9990 chunk 452 optimal weight: 50.0000 chunk 460 optimal weight: 50.0000 chunk 344 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 277 optimal weight: 50.0000 chunk 360 optimal weight: 40.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN E 229 HIS F 221 GLN ** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN F 344 HIS ** G 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 GLN ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.075071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.056179 restraints weight = 385312.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.056253 restraints weight = 294555.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.057302 restraints weight = 211820.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.057537 restraints weight = 139349.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.057712 restraints weight = 123808.322| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 39905 Z= 0.178 Angle : 0.610 14.992 55322 Z= 0.322 Chirality : 0.040 0.206 6487 Planarity : 0.005 0.110 6100 Dihedral : 22.649 127.368 8099 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.93 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.12), residues: 4393 helix: 1.08 (0.11), residues: 2164 sheet: 0.62 (0.19), residues: 618 loop : 0.00 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 29 TYR 0.046 0.002 TYR P 83 PHE 0.029 0.002 PHE I 104 TRP 0.028 0.002 TRP F 283 HIS 0.009 0.002 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.18 (39901) covalent geometry : angle 0.60484 / 0.32 (55316) hydrogen bonds : bond 0.04557 / 3.04 ( 1744) hydrogen bonds : angle 4.01277 / 2.79 ( 4841) metal coordination : bond 0.01560 / 0.71 ( 4) metal coordination : angle 7.45309 / 3.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 113 MET cc_start: 0.8926 (ttp) cc_final: 0.8439 (ttp) REVERT: A 260 MET cc_start: 0.8889 (ptt) cc_final: 0.8096 (ptt) REVERT: A 278 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8771 (mm-30) REVERT: A 306 MET cc_start: 0.8475 (mtp) cc_final: 0.8082 (ttt) REVERT: A 329 PHE cc_start: 0.9422 (m-80) cc_final: 0.8881 (m-80) REVERT: A 359 MET cc_start: 0.8326 (mtm) cc_final: 0.7996 (mmt) REVERT: A 385 ASN cc_start: 0.9246 (t0) cc_final: 0.8714 (p0) REVERT: B 375 CYS cc_start: 0.9053 (m) cc_final: 0.8809 (m) REVERT: C 191 ILE cc_start: 0.9341 (pt) cc_final: 0.8946 (mp) REVERT: C 259 MET cc_start: 0.9394 (mmm) cc_final: 0.9121 (mmm) REVERT: C 260 MET cc_start: 0.9174 (tpt) cc_final: 0.8322 (tpt) REVERT: C 263 LEU cc_start: 0.9411 (mm) cc_final: 0.9168 (mm) REVERT: C 264 MET cc_start: 0.9265 (mmm) cc_final: 0.8406 (mmm) REVERT: C 286 TYR cc_start: 0.9153 (m-80) cc_final: 0.8689 (m-80) REVERT: C 312 PHE cc_start: 0.9449 (m-10) cc_final: 0.9033 (m-80) REVERT: C 332 ASN cc_start: 0.9277 (p0) cc_final: 0.8888 (p0) REVERT: C 371 MET cc_start: 0.9042 (mtm) cc_final: 0.8547 (mtp) REVERT: D 73 VAL cc_start: 0.9345 (t) cc_final: 0.9128 (p) REVERT: D 119 LEU cc_start: 0.9626 (mt) cc_final: 0.9269 (mt) REVERT: D 123 PHE cc_start: 0.9455 (m-10) cc_final: 0.8951 (m-80) REVERT: D 178 MET cc_start: 0.9478 (mmp) cc_final: 0.9169 (mmm) REVERT: D 193 ILE cc_start: 0.9416 (pt) cc_final: 0.9206 (mp) REVERT: D 274 GLU cc_start: 0.9546 (tm-30) cc_final: 0.9322 (tm-30) REVERT: D 303 MET cc_start: 0.8459 (ppp) cc_final: 0.8079 (ttm) REVERT: D 320 MET cc_start: 0.8915 (mmp) cc_final: 0.8565 (mmm) REVERT: D 382 MET cc_start: 0.9536 (tpt) cc_final: 0.8856 (tpp) REVERT: D 443 MET cc_start: 0.9089 (ptm) cc_final: 0.8516 (ptm) REVERT: D 446 TYR cc_start: 0.8982 (m-80) cc_final: 0.8500 (m-80) REVERT: E 113 MET cc_start: 0.9522 (tpp) cc_final: 0.9089 (tpp) REVERT: E 147 MET cc_start: 0.4039 (pmm) cc_final: 0.3761 (pmm) REVERT: E 182 LYS cc_start: 0.9666 (ptmm) cc_final: 0.9396 (ptpt) REVERT: E 191 ILE cc_start: 0.9187 (pt) cc_final: 0.8673 (pt) REVERT: E 260 MET cc_start: 0.9550 (tmm) cc_final: 0.9295 (tmm) REVERT: E 264 MET cc_start: 0.7901 (mmp) cc_final: 0.7547 (mmp) REVERT: E 359 MET cc_start: 0.9154 (mpp) cc_final: 0.8917 (mpp) REVERT: E 371 MET cc_start: 0.9332 (mtp) cc_final: 0.8437 (mpp) REVERT: F 90 MET cc_start: 0.9225 (ttt) cc_final: 0.9020 (ttt) REVERT: F 174 LEU cc_start: 0.8400 (pt) cc_final: 0.7822 (pt) REVERT: F 218 MET cc_start: 0.8218 (tpp) cc_final: 0.7734 (tpp) REVERT: F 382 MET cc_start: 0.7763 (mmp) cc_final: 0.7365 (mmt) REVERT: F 443 MET cc_start: 0.8040 (ttp) cc_final: 0.7358 (tpt) REVERT: G 901 MET cc_start: 0.9502 (tmm) cc_final: 0.9231 (tmm) REVERT: G 925 ARG cc_start: 0.9520 (mmt-90) cc_final: 0.9195 (mmp80) REVERT: G 1061 TRP cc_start: 0.8046 (t60) cc_final: 0.7829 (t60) REVERT: K 24 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8055 (tm-30) REVERT: K 99 ARG cc_start: 0.6653 (mmt180) cc_final: 0.5386 (mpt180) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.2512 time to fit residues: 155.1842 Evaluate side-chains 292 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 353 optimal weight: 50.0000 chunk 458 optimal weight: 50.0000 chunk 251 optimal weight: 0.7980 chunk 434 optimal weight: 4.9990 chunk 350 optimal weight: 9.9990 chunk 276 optimal weight: 50.0000 chunk 151 optimal weight: 0.2980 chunk 327 optimal weight: 0.0070 chunk 26 optimal weight: 8.9990 chunk 343 optimal weight: 30.0000 chunk 210 optimal weight: 7.9990 overall best weight: 2.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN F 251 ASN F 344 HIS ** G 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.075456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.055067 restraints weight = 381938.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.056279 restraints weight = 261511.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.057076 restraints weight = 193058.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.057566 restraints weight = 152612.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.058035 restraints weight = 127273.413| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 39905 Z= 0.126 Angle : 0.577 12.445 55322 Z= 0.301 Chirality : 0.040 0.245 6487 Planarity : 0.004 0.074 6100 Dihedral : 22.621 127.052 8099 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.66 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.12), residues: 4393 helix: 1.24 (0.11), residues: 2178 sheet: 0.52 (0.19), residues: 644 loop : 0.04 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 392 TYR 0.030 0.001 TYR M 54 PHE 0.026 0.002 PHE J 61 TRP 0.018 0.001 TRP F 283 HIS 0.008 0.001 HIS C 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 (39901) covalent geometry : angle 0.57254 / 0.30 (55316) hydrogen bonds : bond 0.03784 / 2.52 ( 1744) hydrogen bonds : angle 3.89168 / 2.71 ( 4841) metal coordination : bond 0.01110 / 0.51 ( 4) metal coordination : angle 6.74035 / 3.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 113 MET cc_start: 0.8886 (ttp) cc_final: 0.8459 (ttp) REVERT: A 260 MET cc_start: 0.8887 (ptt) cc_final: 0.8617 (ptt) REVERT: A 278 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8713 (mm-30) REVERT: A 329 PHE cc_start: 0.9378 (m-80) cc_final: 0.8877 (m-80) REVERT: A 359 MET cc_start: 0.8169 (mtm) cc_final: 0.7815 (mmt) REVERT: A 385 ASN cc_start: 0.9239 (t0) cc_final: 0.8684 (p0) REVERT: C 191 ILE cc_start: 0.9329 (pt) cc_final: 0.8916 (mp) REVERT: C 259 MET cc_start: 0.9380 (mmm) cc_final: 0.9108 (mmm) REVERT: C 260 MET cc_start: 0.9171 (tpt) cc_final: 0.8299 (tpt) REVERT: C 263 LEU cc_start: 0.9464 (mm) cc_final: 0.9217 (mm) REVERT: C 264 MET cc_start: 0.9289 (mmm) cc_final: 0.8395 (mmm) REVERT: C 279 ILE cc_start: 0.9241 (mt) cc_final: 0.8941 (mt) REVERT: C 286 TYR cc_start: 0.9134 (m-80) cc_final: 0.8666 (m-80) REVERT: C 312 PHE cc_start: 0.9389 (m-10) cc_final: 0.9060 (m-10) REVERT: C 332 ASN cc_start: 0.9238 (p0) cc_final: 0.8793 (p0) REVERT: C 371 MET cc_start: 0.9018 (mtm) cc_final: 0.8546 (mtp) REVERT: D 46 MET cc_start: 0.8949 (tpt) cc_final: 0.8267 (tpt) REVERT: D 73 VAL cc_start: 0.9334 (t) cc_final: 0.9128 (p) REVERT: D 119 LEU cc_start: 0.9645 (mt) cc_final: 0.9199 (mt) REVERT: D 123 PHE cc_start: 0.9501 (m-10) cc_final: 0.8986 (m-80) REVERT: D 178 MET cc_start: 0.9446 (mmp) cc_final: 0.9207 (mmm) REVERT: D 274 GLU cc_start: 0.9551 (tm-30) cc_final: 0.9306 (tm-30) REVERT: D 303 MET cc_start: 0.8410 (ppp) cc_final: 0.8200 (ttm) REVERT: D 308 SER cc_start: 0.9515 (m) cc_final: 0.9200 (p) REVERT: D 320 MET cc_start: 0.8937 (mmp) cc_final: 0.8570 (mmm) REVERT: D 382 MET cc_start: 0.9515 (tpt) cc_final: 0.8856 (tpp) REVERT: D 443 MET cc_start: 0.9069 (ptm) cc_final: 0.8479 (ptm) REVERT: D 446 TYR cc_start: 0.8927 (m-80) cc_final: 0.8471 (m-80) REVERT: E 96 MET cc_start: 0.8885 (tmm) cc_final: 0.8650 (tmm) REVERT: E 113 MET cc_start: 0.9510 (tpp) cc_final: 0.9053 (tpp) REVERT: E 114 GLU cc_start: 0.9129 (tt0) cc_final: 0.8192 (tm-30) REVERT: E 182 LYS cc_start: 0.9640 (ptmm) cc_final: 0.9359 (ptpt) REVERT: E 359 MET cc_start: 0.9187 (mpp) cc_final: 0.8849 (mpp) REVERT: E 364 MET cc_start: 0.9344 (pmm) cc_final: 0.8968 (pmm) REVERT: E 371 MET cc_start: 0.9288 (mtp) cc_final: 0.8662 (mtp) REVERT: F 90 MET cc_start: 0.9267 (ttt) cc_final: 0.9006 (ttt) REVERT: F 134 GLU cc_start: 0.8281 (pm20) cc_final: 0.7752 (tm-30) REVERT: F 218 MET cc_start: 0.8163 (tpp) cc_final: 0.7666 (tpp) REVERT: F 303 MET cc_start: 0.6038 (ppp) cc_final: 0.5582 (ppp) REVERT: F 382 MET cc_start: 0.7745 (mmp) cc_final: 0.7448 (mmt) REVERT: F 443 MET cc_start: 0.8093 (ttp) cc_final: 0.7361 (tpt) REVERT: G 1039 LYS cc_start: 0.8709 (ptpp) cc_final: 0.8453 (pttp) REVERT: G 1061 TRP cc_start: 0.7999 (t60) cc_final: 0.7665 (t60) REVERT: K 24 GLN cc_start: 0.8385 (mm-40) cc_final: 0.7956 (tm-30) REVERT: K 99 ARG cc_start: 0.7221 (mmt180) cc_final: 0.6218 (mpt180) REVERT: P 59 MET cc_start: -0.2278 (mmt) cc_final: -0.2648 (mtt) REVERT: P 80 LEU cc_start: 0.7575 (mt) cc_final: 0.7299 (mt) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.2431 time to fit residues: 150.2509 Evaluate side-chains 297 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 465 optimal weight: 50.0000 chunk 272 optimal weight: 7.9990 chunk 246 optimal weight: 20.0000 chunk 420 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 442 optimal weight: 50.0000 chunk 411 optimal weight: 10.0000 chunk 332 optimal weight: 50.0000 chunk 451 optimal weight: 50.0000 chunk 459 optimal weight: 50.0000 chunk 315 optimal weight: 8.9990 overall best weight: 10.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 HIS ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 HIS ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN E 280 ASN E 348 HIS ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 GLN G 847 HIS G 927 HIS G 928 GLN ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.069283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.051384 restraints weight = 404584.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.051484 restraints weight = 273180.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.051827 restraints weight = 189675.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.052016 restraints weight = 167982.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.052113 restraints weight = 145092.794| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 39905 Z= 0.307 Angle : 0.849 19.279 55322 Z= 0.444 Chirality : 0.046 0.250 6487 Planarity : 0.007 0.095 6100 Dihedral : 23.058 117.213 8099 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 25.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.12), residues: 4393 helix: 0.32 (0.10), residues: 2178 sheet: -0.08 (0.18), residues: 636 loop : -0.38 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 314 TYR 0.038 0.003 TYR K 57 PHE 0.042 0.004 PHE J 61 TRP 0.019 0.003 TRP G 860 HIS 0.022 0.004 HIS L 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.31 (39901) covalent geometry : angle 0.84350 / 0.44 (55316) hydrogen bonds : bond 0.07532 / 5.07 ( 1744) hydrogen bonds : angle 4.62817 / 3.23 ( 4841) metal coordination : bond 0.02629 / 1.21 ( 4) metal coordination : angle 9.19745 / 5.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8911 (ttp) cc_final: 0.8282 (ttp) REVERT: A 260 MET cc_start: 0.9000 (ptt) cc_final: 0.8620 (ptt) REVERT: A 278 GLU cc_start: 0.9305 (mm-30) cc_final: 0.8925 (mm-30) REVERT: A 329 PHE cc_start: 0.9439 (m-80) cc_final: 0.8848 (m-80) REVERT: A 359 MET cc_start: 0.8297 (mtm) cc_final: 0.7920 (tpt) REVERT: A 371 MET cc_start: 0.9546 (mpp) cc_final: 0.9021 (mpp) REVERT: B 20 GLU cc_start: 0.9665 (mm-30) cc_final: 0.9303 (mm-30) REVERT: B 312 LEU cc_start: 0.9425 (mt) cc_final: 0.9208 (mt) REVERT: C 191 ILE cc_start: 0.9546 (pt) cc_final: 0.9008 (mm) REVERT: C 260 MET cc_start: 0.9209 (tpt) cc_final: 0.8179 (tpt) REVERT: C 264 MET cc_start: 0.9300 (mmm) cc_final: 0.8523 (mmm) REVERT: C 286 TYR cc_start: 0.9269 (m-80) cc_final: 0.8646 (m-80) REVERT: C 311 CYS cc_start: 0.9191 (m) cc_final: 0.8950 (m) REVERT: C 312 PHE cc_start: 0.9460 (m-10) cc_final: 0.9251 (m-10) REVERT: C 332 ASN cc_start: 0.9402 (p0) cc_final: 0.8851 (p0) REVERT: C 371 MET cc_start: 0.9262 (mtm) cc_final: 0.8726 (mtp) REVERT: D 62 MET cc_start: 0.9152 (tmm) cc_final: 0.8932 (tmm) REVERT: D 119 LEU cc_start: 0.9739 (mt) cc_final: 0.9506 (mm) REVERT: D 123 PHE cc_start: 0.9613 (m-10) cc_final: 0.9135 (m-80) REVERT: D 178 MET cc_start: 0.9593 (mmp) cc_final: 0.9349 (mmm) REVERT: D 320 MET cc_start: 0.9140 (mmp) cc_final: 0.8775 (mmm) REVERT: D 382 MET cc_start: 0.9641 (tpt) cc_final: 0.9268 (tpp) REVERT: D 443 MET cc_start: 0.9259 (ptm) cc_final: 0.8627 (ptm) REVERT: D 446 TYR cc_start: 0.9130 (m-80) cc_final: 0.8774 (m-80) REVERT: E 96 MET cc_start: 0.9190 (tmm) cc_final: 0.8959 (tmm) REVERT: E 113 MET cc_start: 0.9541 (tpp) cc_final: 0.9223 (tpp) REVERT: E 114 GLU cc_start: 0.9140 (tt0) cc_final: 0.8219 (tm-30) REVERT: E 260 MET cc_start: 0.9549 (tmm) cc_final: 0.9303 (tmm) REVERT: E 264 MET cc_start: 0.8707 (mmp) cc_final: 0.8377 (mmp) REVERT: E 359 MET cc_start: 0.9271 (mpp) cc_final: 0.8725 (mpp) REVERT: E 371 MET cc_start: 0.9321 (mtp) cc_final: 0.8696 (mtp) REVERT: F 174 LEU cc_start: 0.8266 (pt) cc_final: 0.7721 (pt) REVERT: F 184 LYS cc_start: 0.9384 (ptmm) cc_final: 0.9022 (ptmm) REVERT: F 197 LYS cc_start: 0.9270 (ttpt) cc_final: 0.8936 (tptp) REVERT: F 218 MET cc_start: 0.8442 (tpp) cc_final: 0.7970 (tpp) REVERT: F 443 MET cc_start: 0.8183 (ttp) cc_final: 0.7593 (tpt) REVERT: G 925 ARG cc_start: 0.9619 (mmt-90) cc_final: 0.9323 (mmp80) REVERT: K 24 GLN cc_start: 0.8634 (mm-40) cc_final: 0.7988 (tm-30) REVERT: P 80 LEU cc_start: 0.7474 (mt) cc_final: 0.6757 (mt) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.2469 time to fit residues: 138.6967 Evaluate side-chains 275 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 419 optimal weight: 7.9990 chunk 173 optimal weight: 7.9990 chunk 465 optimal weight: 50.0000 chunk 204 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 359 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 182 optimal weight: 20.0000 chunk 378 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS A 348 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 348 HIS ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN F 146 GLN ** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN F 344 HIS G 940 HIS I 76 GLN L 82 HIS ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.071197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.051141 restraints weight = 391854.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.052144 restraints weight = 268412.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.052761 restraints weight = 200249.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.053499 restraints weight = 157125.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.053889 restraints weight = 132001.721| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 39905 Z= 0.154 Angle : 0.631 16.080 55322 Z= 0.330 Chirality : 0.042 0.342 6487 Planarity : 0.004 0.064 6100 Dihedral : 22.987 118.922 8099 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.25 % Favored : 97.70 % Rotamer: Outliers : 0.03 % Allowed : 0.75 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.12), residues: 4393 helix: 0.90 (0.11), residues: 2177 sheet: -0.08 (0.19), residues: 610 loop : -0.23 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 945 TYR 0.038 0.002 TYR P 83 PHE 0.027 0.002 PHE J 61 TRP 0.017 0.002 TRP G1085 HIS 0.009 0.001 HIS B 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (39901) covalent geometry : angle 0.62404 / 0.33 (55316) hydrogen bonds : bond 0.04321 / 2.88 ( 1744) hydrogen bonds : angle 4.10786 / 2.86 ( 4841) metal coordination : bond 0.01463 / 0.67 ( 4) metal coordination : angle 8.74420 / 4.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 342 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.9043 (ttp) cc_final: 0.8600 (ttp) REVERT: A 278 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8821 (mm-30) REVERT: A 329 PHE cc_start: 0.9441 (m-80) cc_final: 0.9024 (m-80) REVERT: A 359 MET cc_start: 0.8083 (mtm) cc_final: 0.7713 (tpt) REVERT: A 371 MET cc_start: 0.9508 (mpp) cc_final: 0.8963 (mpp) REVERT: B 20 GLU cc_start: 0.9627 (mm-30) cc_final: 0.9322 (mm-30) REVERT: B 375 CYS cc_start: 0.9213 (m) cc_final: 0.8999 (m) REVERT: C 61 MET cc_start: 0.8302 (mmp) cc_final: 0.7617 (tpp) REVERT: C 191 ILE cc_start: 0.9512 (pt) cc_final: 0.8984 (mm) REVERT: C 260 MET cc_start: 0.9168 (tpt) cc_final: 0.8123 (tpt) REVERT: C 264 MET cc_start: 0.9228 (mmm) cc_final: 0.8428 (mmm) REVERT: C 286 TYR cc_start: 0.9128 (m-80) cc_final: 0.8604 (m-80) REVERT: C 312 PHE cc_start: 0.9409 (m-10) cc_final: 0.9098 (m-10) REVERT: C 329 PHE cc_start: 0.9558 (m-80) cc_final: 0.9296 (m-80) REVERT: C 332 ASN cc_start: 0.9363 (p0) cc_final: 0.8729 (p0) REVERT: C 371 MET cc_start: 0.9196 (mtm) cc_final: 0.8706 (mtp) REVERT: D 88 MET cc_start: 0.9182 (mmp) cc_final: 0.8762 (mmm) REVERT: D 119 LEU cc_start: 0.9721 (mt) cc_final: 0.9345 (mt) REVERT: D 123 PHE cc_start: 0.9568 (m-10) cc_final: 0.9103 (m-80) REVERT: D 178 MET cc_start: 0.9531 (mmp) cc_final: 0.9241 (mmp) REVERT: D 274 GLU cc_start: 0.9552 (tm-30) cc_final: 0.9328 (tm-30) REVERT: D 320 MET cc_start: 0.9228 (mmp) cc_final: 0.8746 (mmm) REVERT: D 382 MET cc_start: 0.9607 (tpt) cc_final: 0.9231 (tpp) REVERT: D 443 MET cc_start: 0.9223 (ptm) cc_final: 0.8673 (ptm) REVERT: D 446 TYR cc_start: 0.9114 (m-80) cc_final: 0.8744 (m-80) REVERT: E 113 MET cc_start: 0.9499 (tpp) cc_final: 0.9186 (tpp) REVERT: E 182 LYS cc_start: 0.9655 (ptmm) cc_final: 0.9454 (ptpt) REVERT: E 256 ILE cc_start: 0.9573 (pt) cc_final: 0.8822 (pt) REVERT: E 359 MET cc_start: 0.9268 (mpp) cc_final: 0.8756 (mpp) REVERT: E 371 MET cc_start: 0.9264 (mtp) cc_final: 0.8666 (mtp) REVERT: F 90 MET cc_start: 0.9352 (ttt) cc_final: 0.8953 (tpt) REVERT: F 168 MET cc_start: 0.8114 (mtm) cc_final: 0.6891 (mpp) REVERT: F 174 LEU cc_start: 0.8191 (pt) cc_final: 0.7404 (pt) REVERT: F 218 MET cc_start: 0.8332 (tpp) cc_final: 0.7809 (tpp) REVERT: F 265 THR cc_start: 0.8022 (t) cc_final: 0.7780 (t) REVERT: F 443 MET cc_start: 0.8104 (ttp) cc_final: 0.7409 (tpt) REVERT: K 24 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7685 (tm-30) outliers start: 1 outliers final: 0 residues processed: 343 average time/residue: 0.2286 time to fit residues: 131.2093 Evaluate side-chains 273 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 380 optimal weight: 40.0000 chunk 305 optimal weight: 4.9990 chunk 287 optimal weight: 0.8980 chunk 225 optimal weight: 6.9990 chunk 268 optimal weight: 0.0870 chunk 183 optimal weight: 7.9990 chunk 193 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 466 optimal weight: 50.0000 chunk 448 optimal weight: 50.0000 chunk 176 optimal weight: 5.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 GLN D 41 GLN E 13 GLN E 115 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN ** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 GLN G 940 HIS L 82 HIS ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.071424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.051466 restraints weight = 392310.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.052411 restraints weight = 269112.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.053079 restraints weight = 197821.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053743 restraints weight = 154822.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.054296 restraints weight = 126719.331| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 39905 Z= 0.136 Angle : 0.606 15.486 55322 Z= 0.315 Chirality : 0.041 0.284 6487 Planarity : 0.004 0.065 6100 Dihedral : 22.843 122.556 8099 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.64 % Favored : 97.31 % Rotamer: Outliers : 0.06 % Allowed : 0.36 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.12), residues: 4393 helix: 1.15 (0.11), residues: 2166 sheet: -0.01 (0.19), residues: 618 loop : -0.12 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 249 TYR 0.029 0.002 TYR M 54 PHE 0.028 0.002 PHE J 61 TRP 0.019 0.002 TRP G 913 HIS 0.022 0.001 HIS L 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (39901) covalent geometry : angle 0.60014 / 0.32 (55316) hydrogen bonds : bond 0.04105 / 2.72 ( 1744) hydrogen bonds : angle 3.97981 / 2.78 ( 4841) metal coordination : bond 0.01281 / 0.58 ( 4) metal coordination : angle 7.87089 / 4.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 330 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8995 (ttp) cc_final: 0.8452 (ttp) REVERT: A 260 MET cc_start: 0.8871 (ptt) cc_final: 0.8442 (ptt) REVERT: A 278 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8823 (mm-30) REVERT: A 329 PHE cc_start: 0.9426 (m-80) cc_final: 0.8910 (m-80) REVERT: A 359 MET cc_start: 0.8036 (mtm) cc_final: 0.7606 (tpt) REVERT: B 20 GLU cc_start: 0.9623 (mm-30) cc_final: 0.9302 (mm-30) REVERT: B 375 CYS cc_start: 0.9300 (m) cc_final: 0.9068 (m) REVERT: C 61 MET cc_start: 0.8624 (mmp) cc_final: 0.7939 (tpp) REVERT: C 96 MET cc_start: 0.8472 (tpp) cc_final: 0.8016 (tpp) REVERT: C 191 ILE cc_start: 0.9514 (pt) cc_final: 0.8961 (mm) REVERT: C 247 ASN cc_start: 0.8425 (m-40) cc_final: 0.8055 (m110) REVERT: C 260 MET cc_start: 0.9185 (tpt) cc_final: 0.8133 (tpp) REVERT: C 264 MET cc_start: 0.9212 (mmm) cc_final: 0.8551 (mmm) REVERT: C 286 TYR cc_start: 0.9173 (m-80) cc_final: 0.8631 (m-80) REVERT: C 311 CYS cc_start: 0.9185 (m) cc_final: 0.8896 (m) REVERT: C 312 PHE cc_start: 0.9412 (m-10) cc_final: 0.9186 (m-10) REVERT: C 316 HIS cc_start: 0.8955 (m90) cc_final: 0.8678 (m-70) REVERT: C 329 PHE cc_start: 0.9575 (m-80) cc_final: 0.9318 (m-80) REVERT: C 332 ASN cc_start: 0.9369 (p0) cc_final: 0.8743 (p0) REVERT: C 371 MET cc_start: 0.9181 (mtm) cc_final: 0.8714 (mtp) REVERT: D 46 MET cc_start: 0.9215 (tpt) cc_final: 0.8448 (tpt) REVERT: D 88 MET cc_start: 0.9180 (mmp) cc_final: 0.8764 (mmm) REVERT: D 113 MET cc_start: 0.6832 (tmm) cc_final: 0.6382 (tmm) REVERT: D 119 LEU cc_start: 0.9720 (mt) cc_final: 0.9360 (mt) REVERT: D 123 PHE cc_start: 0.9558 (m-10) cc_final: 0.9087 (m-80) REVERT: D 274 GLU cc_start: 0.9551 (tm-30) cc_final: 0.9325 (tm-30) REVERT: D 308 SER cc_start: 0.9507 (m) cc_final: 0.9164 (p) REVERT: D 320 MET cc_start: 0.9210 (mmp) cc_final: 0.8665 (mmm) REVERT: D 382 MET cc_start: 0.9569 (tpt) cc_final: 0.9193 (tpp) REVERT: D 443 MET cc_start: 0.9184 (ptm) cc_final: 0.8629 (ptm) REVERT: D 446 TYR cc_start: 0.9111 (m-80) cc_final: 0.8730 (m-80) REVERT: E 13 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8128 (pp30) REVERT: E 113 MET cc_start: 0.9497 (tpp) cc_final: 0.9196 (tpp) REVERT: E 256 ILE cc_start: 0.9219 (pt) cc_final: 0.9014 (pt) REVERT: E 264 MET cc_start: 0.8408 (mmp) cc_final: 0.8200 (mmp) REVERT: E 359 MET cc_start: 0.9252 (mpp) cc_final: 0.8737 (mpp) REVERT: E 371 MET cc_start: 0.9273 (mtp) cc_final: 0.8648 (mtp) REVERT: F 62 MET cc_start: 0.9451 (mmm) cc_final: 0.8947 (mmm) REVERT: F 90 MET cc_start: 0.9449 (ttt) cc_final: 0.9072 (tpt) REVERT: F 174 LEU cc_start: 0.7999 (pt) cc_final: 0.7631 (pt) REVERT: F 218 MET cc_start: 0.8333 (tpp) cc_final: 0.7786 (tpp) REVERT: F 382 MET cc_start: 0.7886 (mmp) cc_final: 0.7628 (mmm) REVERT: F 443 MET cc_start: 0.8101 (ttp) cc_final: 0.7361 (tpt) REVERT: G 925 ARG cc_start: 0.9594 (mmt-90) cc_final: 0.9246 (mmp80) REVERT: K 24 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7678 (tm-30) outliers start: 2 outliers final: 0 residues processed: 332 average time/residue: 0.2353 time to fit residues: 131.6689 Evaluate side-chains 274 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 100 optimal weight: 8.9990 chunk 363 optimal weight: 10.0000 chunk 324 optimal weight: 50.0000 chunk 388 optimal weight: 8.9990 chunk 326 optimal weight: 40.0000 chunk 381 optimal weight: 5.9990 chunk 437 optimal weight: 50.0000 chunk 403 optimal weight: 0.5980 chunk 261 optimal weight: 40.0000 chunk 335 optimal weight: 8.9990 chunk 413 optimal weight: 2.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN F 221 GLN ** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN F 344 HIS G 940 HIS I 108 ASN ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.069818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.050667 restraints weight = 396221.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.051142 restraints weight = 273926.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.051812 restraints weight = 198692.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.052436 restraints weight = 155378.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.052872 restraints weight = 125165.939| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 39905 Z= 0.182 Angle : 0.641 14.125 55322 Z= 0.337 Chirality : 0.042 0.231 6487 Planarity : 0.004 0.066 6100 Dihedral : 22.863 121.772 8099 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.74 % Rotamer: Outliers : 0.03 % Allowed : 0.23 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.12), residues: 4393 helix: 1.00 (0.11), residues: 2197 sheet: -0.05 (0.20), residues: 608 loop : -0.24 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG G 857 TYR 0.021 0.002 TYR P 37 PHE 0.026 0.002 PHE J 61 TRP 0.020 0.002 TRP G1085 HIS 0.015 0.002 HIS L 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (39901) covalent geometry : angle 0.63599 / 0.34 (55316) hydrogen bonds : bond 0.04717 / 3.15 ( 1744) hydrogen bonds : angle 4.09795 / 2.87 ( 4841) metal coordination : bond 0.01707 / 0.79 ( 4) metal coordination : angle 7.93406 / 4.24 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8786 Ramachandran restraints generated. 4393 Oldfield, 0 Emsley, 4393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8970 (ttp) cc_final: 0.8355 (ttp) REVERT: A 260 MET cc_start: 0.8850 (ptt) cc_final: 0.8420 (ptt) REVERT: A 329 PHE cc_start: 0.9461 (m-80) cc_final: 0.8945 (m-80) REVERT: A 359 MET cc_start: 0.8023 (mtm) cc_final: 0.7612 (tpt) REVERT: A 371 MET cc_start: 0.9498 (mpp) cc_final: 0.8960 (mpp) REVERT: B 20 GLU cc_start: 0.9614 (mm-30) cc_final: 0.9326 (mm-30) REVERT: B 375 CYS cc_start: 0.9355 (m) cc_final: 0.9149 (m) REVERT: C 61 MET cc_start: 0.8827 (mmp) cc_final: 0.8098 (tpp) REVERT: C 247 ASN cc_start: 0.8546 (m-40) cc_final: 0.8175 (m110) REVERT: C 259 MET cc_start: 0.9408 (mmm) cc_final: 0.9004 (tpp) REVERT: C 260 MET cc_start: 0.9208 (tpt) cc_final: 0.8160 (tpt) REVERT: C 264 MET cc_start: 0.9188 (mmm) cc_final: 0.8274 (mmm) REVERT: C 286 TYR cc_start: 0.9275 (m-80) cc_final: 0.8703 (m-80) REVERT: C 311 CYS cc_start: 0.9124 (m) cc_final: 0.8787 (m) REVERT: C 312 PHE cc_start: 0.9436 (m-10) cc_final: 0.9091 (m-10) REVERT: C 329 PHE cc_start: 0.9622 (m-80) cc_final: 0.9261 (m-80) REVERT: C 332 ASN cc_start: 0.9429 (p0) cc_final: 0.8835 (p0) REVERT: C 371 MET cc_start: 0.9230 (mtm) cc_final: 0.8726 (mtp) REVERT: D 88 MET cc_start: 0.9280 (mmp) cc_final: 0.8949 (mmm) REVERT: D 113 MET cc_start: 0.6927 (tmm) cc_final: 0.6503 (tmm) REVERT: D 119 LEU cc_start: 0.9710 (mt) cc_final: 0.9386 (mt) REVERT: D 123 PHE cc_start: 0.9574 (m-10) cc_final: 0.9124 (m-80) REVERT: D 274 GLU cc_start: 0.9583 (tm-30) cc_final: 0.9369 (tm-30) REVERT: D 308 SER cc_start: 0.9555 (m) cc_final: 0.9192 (p) REVERT: D 320 MET cc_start: 0.9227 (mmp) cc_final: 0.8722 (mmm) REVERT: D 382 MET cc_start: 0.9554 (tpt) cc_final: 0.9288 (tpp) REVERT: D 443 MET cc_start: 0.9226 (ptm) cc_final: 0.8747 (ptm) REVERT: D 446 TYR cc_start: 0.9090 (m-80) cc_final: 0.8718 (m-80) REVERT: E 113 MET cc_start: 0.9522 (tpp) cc_final: 0.9225 (tpp) REVERT: E 259 MET cc_start: 0.9617 (ptp) cc_final: 0.9287 (ptp) REVERT: E 260 MET cc_start: 0.9493 (tmm) cc_final: 0.9013 (tpt) REVERT: E 264 MET cc_start: 0.8381 (mmp) cc_final: 0.8117 (mmp) REVERT: E 359 MET cc_start: 0.9263 (mpp) cc_final: 0.8740 (mpp) REVERT: E 371 MET cc_start: 0.9286 (mtp) cc_final: 0.8684 (mtp) REVERT: F 184 LYS cc_start: 0.9338 (ptmm) cc_final: 0.9020 (ptmm) REVERT: F 218 MET cc_start: 0.8335 (tpp) cc_final: 0.7806 (tpp) REVERT: F 382 MET cc_start: 0.7996 (mmp) cc_final: 0.7757 (mmm) REVERT: F 443 MET cc_start: 0.8164 (ttp) cc_final: 0.7386 (tpt) REVERT: G 1039 LYS cc_start: 0.9019 (ptpp) cc_final: 0.8794 (pttp) REVERT: K 24 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7731 (tm-30) REVERT: L 73 ILE cc_start: 0.8120 (mt) cc_final: 0.7769 (tp) REVERT: P 80 LEU cc_start: 0.7632 (mt) cc_final: 0.7402 (mt) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.2230 time to fit residues: 121.9522 Evaluate side-chains 269 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 17 optimal weight: 4.9990 chunk 249 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 167 optimal weight: 8.9990 chunk 145 optimal weight: 20.0000 chunk 363 optimal weight: 50.0000 chunk 451 optimal weight: 50.0000 chunk 142 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN ** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN ** F 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 940 HIS L 82 HIS ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 47 GLN ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.073149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.056382 restraints weight = 414588.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.056975 restraints weight = 270668.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.057743 restraints weight = 186164.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.058384 restraints weight = 137159.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.058705 restraints weight = 107488.060| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.6126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 39905 Z= 0.121 Angle : 0.594 14.538 55322 Z= 0.308 Chirality : 0.041 0.232 6487 Planarity : 0.004 0.062 6100 Dihedral : 22.765 121.773 8099 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.60 % Favored : 97.36 % Rotamer: Outliers : 0.03 % Allowed : 0.29 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.13), residues: 4393 helix: 1.31 (0.11), residues: 2170 sheet: 0.03 (0.20), residues: 606 loop : -0.14 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 29 TYR 0.029 0.001 TYR M 54 PHE 0.022 0.001 PHE J 61 TRP 0.022 0.002 TRP G 913 HIS 0.015 0.001 HIS L 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (39901) covalent geometry : angle 0.58850 / 0.31 (55316) hydrogen bonds : bond 0.03792 / 2.52 ( 1744) hydrogen bonds : angle 3.88698 / 2.72 ( 4841) metal coordination : bond 0.01188 / 0.55 ( 4) metal coordination : angle 8.04047 / 4.33 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7624.24 seconds wall clock time: 132 minutes 21.39 seconds (7941.39 seconds total)