Starting phenix.real_space_refine on Sat Mar 7 05:05:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hts_3954/03_2026/6hts_3954.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hts_3954/03_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_3954/03_2026/6hts_3954.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hts_3954/03_2026/6hts_3954.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hts_3954/03_2026/6hts_3954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hts_3954/03_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-dev-5986/lib/python3.9/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: 9.15, 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: 3.27 Conformation dependent library (CDL) restraints added in 1.6 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: 5.05 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: 9.30 Time building geometry restraints manager: 4.40 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 1.460 1.523 -0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" C1' DA Y -5 " pdb=" N9 DA Y -5 " ideal model delta sigma weight residual 1.460 1.519 -0.059 2.00e-02 2.50e+03 8.82e+00 ... (remaining 39896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 54287 1.72 - 3.43: 907 3.43 - 5.15: 88 5.15 - 6.86: 33 6.86 - 8.58: 1 Bond angle restraints: 55316 Sorted by residual: angle pdb=" C THR I 45 " pdb=" N VAL I 46 " pdb=" CA VAL I 46 " ideal model delta sigma weight residual 120.77 125.89 -5.12 1.31e+00 5.83e-01 1.53e+01 angle pdb=" N CYS R 314 " pdb=" CA CYS R 314 " pdb=" C CYS R 314 " ideal model delta sigma weight residual 109.81 118.39 -8.58 2.21e+00 2.05e-01 1.51e+01 angle pdb=" N PRO R 315 " pdb=" CA PRO R 315 " pdb=" C PRO R 315 " ideal model delta sigma weight residual 111.26 117.44 -6.18 1.63e+00 3.76e-01 1.44e+01 angle pdb=" C ARG H 100 " pdb=" N ASN H 101 " pdb=" CA ASN H 101 " ideal model delta sigma weight residual 121.54 127.98 -6.44 1.91e+00 2.74e-01 1.14e+01 angle pdb=" N ILE G 727 " pdb=" CA ILE G 727 " pdb=" C ILE G 727 " ideal model delta sigma weight residual 112.80 109.46 3.34 1.15e+00 7.56e-01 8.46e+00 ... (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: 4369 0.028 - 0.056: 1422 0.056 - 0.084: 333 0.084 - 0.112: 286 0.112 - 0.141: 77 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 44.600 Find NCS groups from input model: 0.780 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:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 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= 0.198 Angle : 0.568 19.500 55322 Z= 0.335 Chirality : 0.037 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 covalent geometry : bond 0.00365 (39901) covalent geometry : angle 0.54521 (55316) hydrogen bonds : bond 0.09348 ( 1744) hydrogen bonds : angle 7.85960 ( 4841) metal coordination : bond 0.16103 ( 4) metal coordination : angle 15.36505 ( 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 : 1.381 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: 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: 0.9121 (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: 0.5656 (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: 0.2739 time to fit residues: 337.7606 Evaluate side-chains 443 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 431 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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: 20.0000 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... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN A 380 GLN ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 B 329 ASN 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 D 233 GLN E 42 GLN E 115 ASN ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN F 240 HIS F 245 HIS F 302 HIS F 344 HIS F 404 GLN G 855 HIS G 927 HIS G 928 GLN I 93 GLN K 112 GLN L 47 GLN L 82 HIS 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 82 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 = 0.3885 r_free = 0.3885 target = 0.080746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.063312 restraints weight = 402087.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.064516 restraints weight = 262634.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.065292 restraints weight = 189729.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.066034 restraints weight = 145355.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.066291 restraints weight = 115763.277| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 39905 Z= 0.169 Angle : 0.600 14.094 55322 Z= 0.318 Chirality : 0.039 0.165 6487 Planarity : 0.005 0.081 6100 Dihedral : 22.342 126.049 8099 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.05 % Favored : 98.93 % Rotamer: Outliers : 0.13 % Allowed : 2.30 % Favored : 97.57 % 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: -0.08 (0.11), residues: 4393 helix: 0.21 (0.10), residues: 2165 sheet: 0.37 (0.18), residues: 612 loop : -0.36 (0.13), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 378 TYR 0.031 0.002 TYR P 37 PHE 0.024 0.002 PHE A 177 TRP 0.010 0.001 TRP G 932 HIS 0.010 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00353 (39901) covalent geometry : angle 0.59449 (55316) hydrogen bonds : bond 0.04285 ( 1744) hydrogen bonds : angle 4.23205 ( 4841) metal coordination : bond 0.01224 ( 4) metal coordination : angle 7.73122 ( 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 473 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 469 time to evaluate : 1.300 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: A 278 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8295 (tm-30) REVERT: A 306 MET cc_start: 0.8565 (mtp) cc_final: 0.8204 (ttm) REVERT: A 329 PHE cc_start: 0.9224 (m-80) cc_final: 0.8862 (m-80) REVERT: A 359 MET cc_start: 0.8122 (mtm) cc_final: 0.7703 (mmt) REVERT: B 377 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8503 (pm20) REVERT: C 57 LYS cc_start: 0.9103 (mtmm) cc_final: 0.8881 (ptpp) REVERT: C 61 MET cc_start: 0.8233 (mmt) cc_final: 0.7905 (tpp) REVERT: C 259 MET cc_start: 0.9411 (mmm) cc_final: 0.9106 (mmm) REVERT: C 260 MET cc_start: 0.9130 (tpt) cc_final: 0.8820 (tpt) REVERT: C 306 MET cc_start: 0.9145 (tpp) cc_final: 0.8685 (tpp) REVERT: C 312 PHE cc_start: 0.9401 (m-10) cc_final: 0.9148 (m-10) REVERT: C 313 THR cc_start: 0.9480 (m) cc_final: 0.9186 (m) REVERT: C 316 HIS cc_start: 0.8939 (m-70) cc_final: 0.8155 (m90) REVERT: C 320 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7926 (mm-30) REVERT: C 371 MET cc_start: 0.8925 (mtm) cc_final: 0.8563 (mtp) REVERT: D 90 MET cc_start: 0.9019 (ptp) cc_final: 0.8728 (ptp) REVERT: D 113 MET cc_start: 0.8591 (ptm) cc_final: 0.8244 (ptm) REVERT: D 178 MET cc_start: 0.9471 (mmp) cc_final: 0.9245 (mmp) REVERT: D 193 ILE cc_start: 0.9380 (pt) cc_final: 0.9033 (mm) REVERT: D 274 GLU cc_start: 0.9492 (tm-30) cc_final: 0.9237 (tm-30) REVERT: D 303 MET cc_start: 0.7775 (ppp) cc_final: 0.6899 (ttm) REVERT: D 382 MET cc_start: 0.9143 (tpt) cc_final: 0.8421 (tpp) REVERT: D 443 MET cc_start: 0.8892 (ptm) cc_final: 0.8179 (ptm) REVERT: E 113 MET cc_start: 0.9520 (tpp) cc_final: 0.9048 (tpp) REVERT: E 182 LYS cc_start: 0.9683 (ptmm) cc_final: 0.9273 (ptpt) REVERT: E 191 ILE cc_start: 0.9342 (pt) cc_final: 0.8899 (pt) REVERT: E 203 GLN cc_start: 0.9251 (tt0) cc_final: 0.8964 (mt0) REVERT: E 259 MET cc_start: 0.9635 (ttm) cc_final: 0.9221 (ttt) REVERT: E 371 MET cc_start: 0.9351 (mtp) cc_final: 0.8444 (mpp) REVERT: F 62 MET cc_start: 0.9301 (ttm) cc_final: 0.9052 (mtt) REVERT: F 174 LEU cc_start: 0.8267 (pt) cc_final: 0.7954 (pt) REVERT: F 382 MET cc_start: 0.8531 (mmp) cc_final: 0.7301 (mmt) REVERT: F 443 MET cc_start: 0.8001 (ttp) cc_final: 0.7260 (tpt) REVERT: G 895 ASP cc_start: 0.9074 (p0) cc_final: 0.8649 (p0) REVERT: G 917 PHE cc_start: 0.9529 (t80) cc_final: 0.9255 (t80) REVERT: G 921 LYS cc_start: 0.9649 (mmpt) cc_final: 0.9431 (mmmt) REVERT: G 1023 ASP cc_start: 0.9194 (p0) cc_final: 0.8868 (t0) REVERT: I 101 VAL cc_start: 0.7287 (t) cc_final: 0.7079 (t) REVERT: K 24 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7949 (tm-30) REVERT: K 99 ARG cc_start: 0.7281 (mmt180) cc_final: 0.6247 (mpt180) REVERT: P 80 LEU cc_start: 0.7232 (mt) cc_final: 0.6666 (mt) outliers start: 4 outliers final: 0 residues processed: 473 average time/residue: 0.2513 time to fit residues: 188.4104 Evaluate side-chains 337 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 336 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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: 10.0000 chunk 455 optimal weight: 20.0000 chunk 424 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 296 optimal weight: 9.9990 chunk 401 optimal weight: 40.0000 chunk 428 optimal weight: 5.9990 chunk 242 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN C 42 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN ** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 HIS F 146 GLN F 344 HIS ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.074781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.054800 restraints weight = 386705.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.056096 restraints weight = 286576.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.056912 restraints weight = 170161.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.057160 restraints weight = 131942.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.057266 restraints weight = 120822.273| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 39905 Z= 0.172 Angle : 0.571 17.521 55322 Z= 0.302 Chirality : 0.038 0.155 6487 Planarity : 0.004 0.078 6100 Dihedral : 22.380 126.366 8099 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.57 % Favored : 98.41 % Rotamer: Outliers : 0.03 % Allowed : 2.53 % 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: 0.67 (0.12), residues: 4393 helix: 0.91 (0.11), residues: 2178 sheet: 0.41 (0.18), residues: 651 loop : -0.03 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 342 TYR 0.024 0.002 TYR M 54 PHE 0.021 0.002 PHE A 213 TRP 0.011 0.002 TRP G1077 HIS 0.007 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00342 (39901) covalent geometry : angle 0.56384 (55316) hydrogen bonds : bond 0.03932 ( 1744) hydrogen bonds : angle 3.99408 ( 4841) metal coordination : bond 0.01445 ( 4) metal coordination : angle 8.87166 ( 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 407 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 406 time to evaluate : 1.320 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: 0.8585 (ptm) REVERT: A 259 MET cc_start: 0.9534 (tpp) cc_final: 0.9265 (tpp) REVERT: A 278 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8731 (mm-30) REVERT: A 306 MET cc_start: 0.8416 (mtp) cc_final: 0.8190 (ttm) REVERT: A 329 PHE cc_start: 0.9343 (m-80) cc_final: 0.8916 (m-80) REVERT: A 359 MET cc_start: 0.8039 (mtm) cc_final: 0.7585 (mmt) REVERT: C 61 MET cc_start: 0.8450 (mmt) cc_final: 0.8097 (tpp) REVERT: C 191 ILE cc_start: 0.9425 (pt) cc_final: 0.8662 (mm) REVERT: C 259 MET cc_start: 0.9393 (mmm) cc_final: 0.9176 (mmm) REVERT: C 260 MET cc_start: 0.9209 (tpt) cc_final: 0.8431 (tpt) REVERT: C 263 LEU cc_start: 0.9435 (mm) cc_final: 0.9178 (mm) REVERT: C 264 MET cc_start: 0.9098 (mmp) cc_final: 0.8054 (mmm) REVERT: C 279 ILE cc_start: 0.9200 (mt) cc_final: 0.8991 (mt) REVERT: C 306 MET cc_start: 0.9108 (tpp) cc_final: 0.8758 (mmt) REVERT: C 312 PHE cc_start: 0.9448 (m-10) cc_final: 0.9225 (m-80) REVERT: C 316 HIS cc_start: 0.8966 (m-70) cc_final: 0.8610 (m90) REVERT: C 320 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8064 (mp0) REVERT: C 332 ASN cc_start: 0.9163 (p0) cc_final: 0.8963 (p0) REVERT: C 371 MET cc_start: 0.9127 (mtm) cc_final: 0.8698 (mtp) REVERT: D 123 PHE cc_start: 0.9529 (m-80) cc_final: 0.9192 (m-80) REVERT: D 172 TYR cc_start: 0.9037 (m-80) cc_final: 0.8444 (m-80) REVERT: D 193 ILE cc_start: 0.9419 (pt) cc_final: 0.9212 (mp) REVERT: D 274 GLU cc_start: 0.9555 (tm-30) cc_final: 0.9336 (tm-30) REVERT: D 303 MET cc_start: 0.8221 (ppp) cc_final: 0.7417 (ttm) REVERT: D 320 MET cc_start: 0.8861 (mmp) cc_final: 0.8459 (mmm) REVERT: D 382 MET cc_start: 0.9463 (tpt) cc_final: 0.8832 (tpp) REVERT: D 443 MET cc_start: 0.9147 (ptm) cc_final: 0.8502 (ptm) REVERT: E 96 MET cc_start: 0.9063 (tmm) cc_final: 0.8821 (tmm) REVERT: E 113 MET cc_start: 0.9571 (tpp) cc_final: 0.9247 (tpp) REVERT: E 182 LYS cc_start: 0.9694 (ptmm) cc_final: 0.9487 (ptpt) REVERT: E 191 ILE cc_start: 0.9445 (pt) cc_final: 0.9023 (pt) REVERT: E 192 TYR cc_start: 0.8528 (t80) cc_final: 0.8237 (t80) REVERT: E 260 MET cc_start: 0.9520 (tmm) cc_final: 0.9269 (tmm) REVERT: E 264 MET cc_start: 0.7829 (mmp) cc_final: 0.7574 (mmp) REVERT: E 371 MET cc_start: 0.9329 (mtp) cc_final: 0.8448 (mpp) REVERT: F 90 MET cc_start: 0.9268 (ttt) cc_final: 0.8848 (tpt) REVERT: F 218 MET cc_start: 0.7788 (mmp) cc_final: 0.7008 (tpp) REVERT: F 246 GLU cc_start: 0.9104 (pt0) cc_final: 0.8436 (mp0) REVERT: F 382 MET cc_start: 0.7654 (mmp) cc_final: 0.7380 (mmm) REVERT: F 443 MET cc_start: 0.8167 (ttp) cc_final: 0.7456 (tpt) REVERT: G 925 ARG cc_start: 0.9637 (mpp-170) cc_final: 0.9298 (mmt-90) REVERT: G 1061 TRP cc_start: 0.7977 (t60) cc_final: 0.7762 (t60) REVERT: K 24 GLN cc_start: 0.8471 (mm-40) cc_final: 0.7989 (tm-30) REVERT: K 99 ARG cc_start: 0.6792 (mmt180) cc_final: 0.5469 (mpt180) REVERT: L 73 ILE cc_start: 0.8131 (mt) cc_final: 0.7887 (tp) REVERT: P 80 LEU cc_start: 0.7543 (mt) cc_final: 0.6642 (mt) outliers start: 1 outliers final: 0 residues processed: 407 average time/residue: 0.2510 time to fit residues: 165.5658 Evaluate side-chains 307 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 311 optimal weight: 20.0000 chunk 287 optimal weight: 5.9990 chunk 342 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 369 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN B 25 HIS ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN F 146 GLN F 251 ASN F 344 HIS ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 GLN N 25 ASN P 49 HIS ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.074597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.057336 restraints weight = 413130.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.058289 restraints weight = 263829.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.059029 restraints weight = 187114.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.059759 restraints weight = 140141.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.060006 restraints weight = 110257.243| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 39905 Z= 0.173 Angle : 0.585 15.193 55322 Z= 0.311 Chirality : 0.039 0.188 6487 Planarity : 0.004 0.071 6100 Dihedral : 22.458 125.492 8099 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.98 % Favored : 98.00 % Rotamer: Outliers : 0.03 % Allowed : 2.53 % 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: 1.15 (0.11), residues: 2190 sheet: 0.42 (0.18), residues: 641 loop : -0.04 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 925 TYR 0.025 0.002 TYR M 54 PHE 0.018 0.002 PHE A 437 TRP 0.021 0.002 TRP G 913 HIS 0.007 0.001 HIS P 82 Details of bonding type rmsd covalent geometry : bond 0.00358 (39901) covalent geometry : angle 0.57918 (55316) hydrogen bonds : bond 0.04135 ( 1744) hydrogen bonds : angle 3.87876 ( 4841) metal coordination : bond 0.01461 ( 4) metal coordination : angle 8.19772 ( 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 369 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 368 time to evaluate : 1.389 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: 0.9102 (ttp) cc_final: 0.8599 (ttp) REVERT: A 278 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8778 (mm-30) REVERT: A 329 PHE cc_start: 0.9290 (m-80) cc_final: 0.8903 (m-80) REVERT: A 359 MET cc_start: 0.7970 (mtm) cc_final: 0.7570 (tpt) REVERT: C 61 MET cc_start: 0.8541 (mmt) cc_final: 0.8143 (tpp) REVERT: C 191 ILE cc_start: 0.9445 (pt) cc_final: 0.8885 (mm) REVERT: C 260 MET cc_start: 0.9241 (tpt) cc_final: 0.8460 (tpt) REVERT: C 264 MET cc_start: 0.9244 (mmp) cc_final: 0.8131 (mmm) REVERT: C 286 TYR cc_start: 0.9241 (m-80) cc_final: 0.8671 (m-80) REVERT: C 316 HIS cc_start: 0.8995 (m-70) cc_final: 0.8490 (m90) REVERT: C 332 ASN cc_start: 0.9359 (p0) cc_final: 0.8807 (p0) REVERT: C 371 MET cc_start: 0.9158 (mtm) cc_final: 0.8742 (mtp) REVERT: D 123 PHE cc_start: 0.9534 (m-80) cc_final: 0.9308 (m-80) REVERT: D 178 MET cc_start: 0.9417 (mmp) cc_final: 0.9162 (mmm) REVERT: D 193 ILE cc_start: 0.9390 (pt) cc_final: 0.9171 (mp) REVERT: D 274 GLU cc_start: 0.9477 (tm-30) cc_final: 0.9230 (tm-30) REVERT: D 303 MET cc_start: 0.8532 (ppp) cc_final: 0.7884 (ttm) REVERT: D 320 MET cc_start: 0.8995 (mmp) cc_final: 0.8565 (mmm) REVERT: D 326 MET cc_start: 0.9536 (mtt) cc_final: 0.9197 (mtt) REVERT: D 382 MET cc_start: 0.9533 (tpt) cc_final: 0.9050 (tpp) REVERT: D 443 MET cc_start: 0.9219 (ptm) cc_final: 0.8613 (ptm) REVERT: D 446 TYR cc_start: 0.9131 (m-80) cc_final: 0.8774 (m-80) REVERT: E 61 MET cc_start: 0.8921 (mmm) cc_final: 0.8260 (tpt) REVERT: E 96 MET cc_start: 0.9005 (tmm) cc_final: 0.8796 (tmm) REVERT: E 113 MET cc_start: 0.9535 (tpp) cc_final: 0.9233 (tpp) REVERT: E 182 LYS cc_start: 0.9675 (ptmm) cc_final: 0.9398 (ptpt) REVERT: E 260 MET cc_start: 0.9491 (tmm) cc_final: 0.9240 (tmm) REVERT: E 264 MET cc_start: 0.8137 (mmp) cc_final: 0.7888 (mmp) REVERT: E 359 MET cc_start: 0.9201 (mpp) cc_final: 0.8889 (mpp) REVERT: E 364 MET cc_start: 0.9235 (pmm) cc_final: 0.8901 (pmm) REVERT: E 371 MET cc_start: 0.9308 (mtp) cc_final: 0.8649 (mtp) REVERT: F 90 MET cc_start: 0.9337 (ttt) cc_final: 0.9120 (ttt) REVERT: F 197 LYS cc_start: 0.9178 (ttpt) cc_final: 0.8905 (tptp) REVERT: F 382 MET cc_start: 0.7948 (mmp) cc_final: 0.7379 (mmt) REVERT: F 443 MET cc_start: 0.8179 (ttp) cc_final: 0.7425 (tpt) REVERT: G 925 ARG cc_start: 0.9691 (mpp-170) cc_final: 0.9408 (mmt-90) REVERT: G 1061 TRP cc_start: 0.7900 (t60) cc_final: 0.7646 (t60) REVERT: K 24 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7767 (tm-30) REVERT: P 80 LEU cc_start: 0.7742 (mt) cc_final: 0.7286 (mt) outliers start: 1 outliers final: 0 residues processed: 369 average time/residue: 0.2455 time to fit residues: 147.9399 Evaluate side-chains 291 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.557 ------------------------------------------------------------------------------- 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: 8.9990 chunk 464 optimal weight: 20.0000 chunk 150 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 280 optimal weight: 20.0000 chunk 452 optimal weight: 20.0000 chunk 460 optimal weight: 30.0000 chunk 344 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 chunk 277 optimal weight: 50.0000 chunk 360 optimal weight: 30.0000 overall best weight: 13.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 HIS ** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN D 41 GLN D 329 ASN ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 HIS ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 847 HIS ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1027 ASN I 76 GLN I 108 ASN L 47 GLN L 82 HIS ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 47 GLN ** P 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 327 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.064953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.046657 restraints weight = 418221.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.047499 restraints weight = 293457.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.047891 restraints weight = 182065.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048025 restraints weight = 159540.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048043 restraints weight = 140675.739| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.7451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.191 39905 Z= 0.396 Angle : 0.922 31.353 55322 Z= 0.492 Chirality : 0.047 0.262 6487 Planarity : 0.007 0.106 6100 Dihedral : 23.481 107.251 8099 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 30.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 0.19 % Allowed : 3.15 % Favored : 96.66 % 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: -0.61 (0.12), residues: 4393 helix: -0.06 (0.10), residues: 2163 sheet: -0.45 (0.18), residues: 636 loop : -0.64 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 21 TYR 0.037 0.003 TYR E 286 PHE 0.040 0.004 PHE G1068 TRP 0.018 0.003 TRP G 913 HIS 0.014 0.003 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00794 (39901) covalent geometry : angle 0.90902 (55316) hydrogen bonds : bond 0.07880 ( 1744) hydrogen bonds : angle 5.11006 ( 4841) metal coordination : bond 0.02926 ( 4) metal coordination : angle 14.75224 ( 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 339 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 333 time to evaluate : 1.409 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: 0.8936 (ttp) cc_final: 0.8455 (ttp) REVERT: A 359 MET cc_start: 0.7875 (mtm) cc_final: 0.7469 (tpt) REVERT: B 20 GLU cc_start: 0.9618 (mm-30) cc_final: 0.9414 (tp30) REVERT: B 63 ILE cc_start: 0.9746 (mt) cc_final: 0.9426 (mt) REVERT: B 103 ILE cc_start: 0.9423 (tp) cc_final: 0.9123 (tp) REVERT: B 316 LEU cc_start: 0.9052 (mt) cc_final: 0.8790 (tt) REVERT: C 61 MET cc_start: 0.8746 (mmt) cc_final: 0.8379 (tpp) REVERT: C 158 ILE cc_start: 0.8283 (mm) cc_final: 0.7952 (tp) REVERT: C 260 MET cc_start: 0.9391 (tpt) cc_final: 0.8643 (tpp) REVERT: C 264 MET cc_start: 0.9293 (mmp) cc_final: 0.8603 (mmm) REVERT: C 286 TYR cc_start: 0.9467 (m-80) cc_final: 0.8863 (m-80) REVERT: C 317 ARG cc_start: 0.9410 (ttt180) cc_final: 0.9143 (tpt170) REVERT: C 332 ASN cc_start: 0.9503 (p0) cc_final: 0.9198 (p0) REVERT: C 371 MET cc_start: 0.9418 (mtm) cc_final: 0.8921 (mtp) REVERT: D 88 MET cc_start: 0.9266 (mmp) cc_final: 0.8936 (mmm) REVERT: D 113 MET cc_start: 0.9004 (ptm) cc_final: 0.7788 (tmm) REVERT: D 303 MET cc_start: 0.8683 (ppp) cc_final: 0.8344 (ttm) REVERT: D 320 MET cc_start: 0.9400 (mmp) cc_final: 0.9012 (mmm) REVERT: D 382 MET cc_start: 0.9529 (tpt) cc_final: 0.8972 (mmm) REVERT: D 446 TYR cc_start: 0.9109 (m-80) cc_final: 0.8814 (m-80) REVERT: E 113 MET cc_start: 0.9560 (tpp) cc_final: 0.9290 (tpp) REVERT: E 259 MET cc_start: 0.9751 (ttm) cc_final: 0.9427 (ttt) REVERT: E 260 MET cc_start: 0.9572 (tmm) cc_final: 0.9066 (tpt) REVERT: E 264 MET cc_start: 0.9031 (mmp) cc_final: 0.8317 (mmp) REVERT: E 359 MET cc_start: 0.9260 (mpp) cc_final: 0.8804 (mpp) REVERT: E 371 MET cc_start: 0.9285 (mtp) cc_final: 0.8654 (mtp) REVERT: F 90 MET cc_start: 0.9368 (ttt) cc_final: 0.9109 (ttt) REVERT: F 303 MET cc_start: 0.7864 (ppp) cc_final: 0.7329 (ppp) REVERT: F 443 MET cc_start: 0.8383 (ttp) cc_final: 0.7729 (tpt) REVERT: G 1061 TRP cc_start: 0.7446 (t60) cc_final: 0.7141 (t60) REVERT: M 120 MET cc_start: -0.4350 (mmt) cc_final: -0.4601 (mmt) REVERT: P 80 LEU cc_start: 0.8565 (mt) cc_final: 0.8330 (mt) REVERT: R 301 SER cc_start: 0.8672 (p) cc_final: 0.8472 (t) outliers start: 6 outliers final: 4 residues processed: 338 average time/residue: 0.2474 time to fit residues: 136.9772 Evaluate side-chains 249 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 245 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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: 20.0000 chunk 458 optimal weight: 10.0000 chunk 251 optimal weight: 20.0000 chunk 434 optimal weight: 20.0000 chunk 350 optimal weight: 50.0000 chunk 276 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 327 optimal weight: 50.0000 chunk 26 optimal weight: 5.9990 chunk 343 optimal weight: 6.9990 chunk 210 optimal weight: 8.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A 429 HIS ** 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 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 HIS ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 940 HIS L 82 HIS ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 ASN O 38 ASN O 68 ASN ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 47 GLN P 49 HIS ** P 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.065698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.048230 restraints weight = 410614.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048410 restraints weight = 251499.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.048647 restraints weight = 178321.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.048794 restraints weight = 154580.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.048835 restraints weight = 140582.822| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.7783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 39905 Z= 0.247 Angle : 0.714 28.082 55322 Z= 0.379 Chirality : 0.042 0.245 6487 Planarity : 0.005 0.070 6100 Dihedral : 23.370 118.117 8099 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.80 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: -0.40 (0.12), residues: 4393 helix: 0.29 (0.11), residues: 2182 sheet: -0.56 (0.19), residues: 666 loop : -0.72 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 314 TYR 0.031 0.002 TYR P 83 PHE 0.018 0.002 PHE F 209 TRP 0.019 0.002 TRP G 913 HIS 0.018 0.002 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00502 (39901) covalent geometry : angle 0.70023 (55316) hydrogen bonds : bond 0.05641 ( 1744) hydrogen bonds : angle 4.57254 ( 4841) metal coordination : bond 0.02233 ( 4) metal coordination : angle 13.40473 ( 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 318 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.9066 (ttp) cc_final: 0.8796 (ttp) REVERT: A 359 MET cc_start: 0.7895 (mtm) cc_final: 0.7384 (tpp) REVERT: A 371 MET cc_start: 0.9569 (mpp) cc_final: 0.9026 (mpp) REVERT: B 20 GLU cc_start: 0.9625 (mm-30) cc_final: 0.9359 (tp30) REVERT: B 22 ILE cc_start: 0.8840 (tt) cc_final: 0.8570 (pt) REVERT: B 62 MET cc_start: 0.9271 (tmm) cc_final: 0.9043 (tmm) REVERT: B 63 ILE cc_start: 0.9734 (mt) cc_final: 0.9309 (mt) REVERT: B 103 ILE cc_start: 0.9596 (tp) cc_final: 0.9267 (tp) REVERT: C 61 MET cc_start: 0.8623 (mmt) cc_final: 0.8280 (tpp) REVERT: C 165 LYS cc_start: 0.9323 (tptm) cc_final: 0.8876 (tptp) REVERT: C 178 GLU cc_start: 0.9801 (tt0) cc_final: 0.9354 (mm-30) REVERT: C 264 MET cc_start: 0.9265 (mmp) cc_final: 0.9061 (mmm) REVERT: C 286 TYR cc_start: 0.9499 (m-80) cc_final: 0.8929 (m-80) REVERT: C 311 CYS cc_start: 0.9227 (m) cc_final: 0.8906 (m) REVERT: C 317 ARG cc_start: 0.9418 (ttt180) cc_final: 0.9193 (tpt170) REVERT: C 319 LEU cc_start: 0.9724 (mm) cc_final: 0.9470 (tp) REVERT: C 371 MET cc_start: 0.9416 (mtm) cc_final: 0.8925 (mtp) REVERT: D 88 MET cc_start: 0.9322 (mmp) cc_final: 0.8976 (mmm) REVERT: D 123 PHE cc_start: 0.9594 (m-80) cc_final: 0.9307 (m-80) REVERT: D 303 MET cc_start: 0.8707 (ppp) cc_final: 0.8152 (ttm) REVERT: D 320 MET cc_start: 0.9376 (mmp) cc_final: 0.8958 (mmm) REVERT: D 382 MET cc_start: 0.9407 (tpt) cc_final: 0.9124 (mmm) REVERT: D 446 TYR cc_start: 0.9131 (m-80) cc_final: 0.8820 (m-80) REVERT: E 113 MET cc_start: 0.9554 (tpp) cc_final: 0.9294 (tpp) REVERT: E 182 LYS cc_start: 0.9678 (ptmm) cc_final: 0.9345 (ptpt) REVERT: E 259 MET cc_start: 0.9771 (ttm) cc_final: 0.9516 (ttt) REVERT: E 260 MET cc_start: 0.9575 (tmm) cc_final: 0.9065 (tpt) REVERT: E 264 MET cc_start: 0.8976 (mmp) cc_final: 0.8180 (mmp) REVERT: E 359 MET cc_start: 0.9306 (mpp) cc_final: 0.8936 (mpp) REVERT: E 364 MET cc_start: 0.9196 (pmm) cc_final: 0.8993 (pmm) REVERT: E 371 MET cc_start: 0.9166 (mtp) cc_final: 0.8582 (mtp) REVERT: F 303 MET cc_start: 0.7755 (ppp) cc_final: 0.7177 (ppp) REVERT: F 382 MET cc_start: 0.8677 (mmp) cc_final: 0.8364 (mmp) REVERT: F 443 MET cc_start: 0.8403 (ttp) cc_final: 0.7658 (tpt) REVERT: G 1018 THR cc_start: 0.9146 (p) cc_final: 0.8909 (t) REVERT: G 1061 TRP cc_start: 0.7503 (t60) cc_final: 0.7194 (t60) REVERT: M 54 TYR cc_start: 0.5650 (m-80) cc_final: 0.5208 (m-80) REVERT: O 27 VAL cc_start: 0.7213 (m) cc_final: 0.6769 (m) REVERT: P 37 TYR cc_start: 0.8819 (m-80) cc_final: 0.8611 (m-80) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.2552 time to fit residues: 134.1044 Evaluate side-chains 247 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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: 10.0000 chunk 272 optimal weight: 50.0000 chunk 246 optimal weight: 7.9990 chunk 420 optimal weight: 0.4980 chunk 116 optimal weight: 8.9990 chunk 442 optimal weight: 20.0000 chunk 411 optimal weight: 40.0000 chunk 332 optimal weight: 50.0000 chunk 451 optimal weight: 20.0000 chunk 459 optimal weight: 30.0000 chunk 315 optimal weight: 30.0000 overall best weight: 9.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 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** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 HIS ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 GLN ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.064068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.046156 restraints weight = 419209.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.046707 restraints weight = 288586.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.047341 restraints weight = 189016.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.047348 restraints weight = 152262.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.047419 restraints weight = 131124.550| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.8688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 39905 Z= 0.289 Angle : 0.774 29.939 55322 Z= 0.412 Chirality : 0.043 0.233 6487 Planarity : 0.006 0.086 6100 Dihedral : 23.509 120.075 8099 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 25.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.58 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -0.63 (0.12), residues: 4393 helix: 0.20 (0.11), residues: 2197 sheet: -0.91 (0.19), residues: 673 loop : -0.89 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 253 TYR 0.033 0.002 TYR P 83 PHE 0.023 0.003 PHE G 831 TRP 0.021 0.003 TRP G 932 HIS 0.021 0.003 HIS L 109 Details of bonding type rmsd covalent geometry : bond 0.00578 (39901) covalent geometry : angle 0.75895 (55316) hydrogen bonds : bond 0.06323 ( 1744) hydrogen bonds : angle 4.72437 ( 4841) metal coordination : bond 0.02615 ( 4) metal coordination : angle 14.55820 ( 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 317 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.372 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 359 MET cc_start: 0.7686 (mtm) cc_final: 0.7150 (tpp) REVERT: B 20 GLU cc_start: 0.9584 (mm-30) cc_final: 0.9257 (tp30) REVERT: B 62 MET cc_start: 0.9230 (tmm) cc_final: 0.9012 (tmm) REVERT: B 63 ILE cc_start: 0.9744 (mt) cc_final: 0.9320 (mt) REVERT: B 103 ILE cc_start: 0.9636 (tp) cc_final: 0.9333 (tp) REVERT: C 61 MET cc_start: 0.8462 (mmt) cc_final: 0.8184 (mmt) REVERT: C 165 LYS cc_start: 0.9406 (tptm) cc_final: 0.8993 (tptp) REVERT: C 178 GLU cc_start: 0.9794 (tt0) cc_final: 0.9354 (mm-30) REVERT: C 260 MET cc_start: 0.9372 (mtm) cc_final: 0.9029 (tpt) REVERT: C 264 MET cc_start: 0.9470 (mmp) cc_final: 0.8142 (mmm) REVERT: C 286 TYR cc_start: 0.9513 (m-80) cc_final: 0.9016 (m-80) REVERT: C 311 CYS cc_start: 0.9330 (m) cc_final: 0.9122 (m) REVERT: C 312 PHE cc_start: 0.9632 (m-80) cc_final: 0.9253 (m-80) REVERT: C 319 LEU cc_start: 0.9723 (mm) cc_final: 0.9447 (tp) REVERT: C 371 MET cc_start: 0.9439 (mtm) cc_final: 0.8934 (mtp) REVERT: D 88 MET cc_start: 0.9332 (mmp) cc_final: 0.8821 (mmm) REVERT: D 303 MET cc_start: 0.8890 (ppp) cc_final: 0.8086 (ttm) REVERT: D 320 MET cc_start: 0.9396 (mmp) cc_final: 0.9007 (mmm) REVERT: D 382 MET cc_start: 0.9376 (tpt) cc_final: 0.9126 (mmm) REVERT: D 446 TYR cc_start: 0.9132 (m-80) cc_final: 0.8835 (m-80) REVERT: E 113 MET cc_start: 0.9556 (tpp) cc_final: 0.9298 (tpp) REVERT: E 259 MET cc_start: 0.9790 (ttm) cc_final: 0.9538 (ttt) REVERT: E 260 MET cc_start: 0.9557 (tmm) cc_final: 0.9110 (tpt) REVERT: E 264 MET cc_start: 0.9026 (mmp) cc_final: 0.8293 (mmp) REVERT: E 359 MET cc_start: 0.9287 (mpp) cc_final: 0.9064 (mpp) REVERT: E 364 MET cc_start: 0.9053 (pmm) cc_final: 0.8817 (pmm) REVERT: E 371 MET cc_start: 0.9204 (mtp) cc_final: 0.8578 (mtp) REVERT: F 90 MET cc_start: 0.9426 (ttt) cc_final: 0.9173 (tpt) REVERT: F 382 MET cc_start: 0.8725 (mmp) cc_final: 0.8158 (mmt) REVERT: F 443 MET cc_start: 0.8464 (ttp) cc_final: 0.7612 (tpp) REVERT: G 928 GLN cc_start: 0.8700 (mp10) cc_final: 0.8408 (mp10) REVERT: G 1018 THR cc_start: 0.9146 (p) cc_final: 0.8895 (t) REVERT: N 75 HIS cc_start: 0.6148 (t70) cc_final: 0.5811 (t70) REVERT: P 80 LEU cc_start: 0.8698 (mt) cc_final: 0.8339 (mt) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.2438 time to fit residues: 127.5950 Evaluate side-chains 236 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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: 9.9990 chunk 173 optimal weight: 4.9990 chunk 465 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 359 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 182 optimal weight: 0.0470 chunk 378 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 HIS A 380 GLN ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 GLN B 146 GLN B 245 HIS B 447 GLN D 41 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 940 HIS G1027 ASN I 76 GLN ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 ASN L 82 HIS ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.068146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.051429 restraints weight = 425239.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.052156 restraints weight = 262982.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.052866 restraints weight = 184857.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.053559 restraints weight = 139411.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.053787 restraints weight = 109680.683| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.8565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39905 Z= 0.150 Angle : 0.638 22.723 55322 Z= 0.334 Chirality : 0.041 0.221 6487 Planarity : 0.005 0.112 6100 Dihedral : 23.270 122.782 8099 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.23 % Favored : 96.74 % Rotamer: Outliers : 0.03 % Allowed : 0.62 % Favored : 99.35 % 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: -0.03 (0.13), residues: 4393 helix: 0.80 (0.11), residues: 2182 sheet: -0.71 (0.19), residues: 673 loop : -0.73 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 925 TYR 0.038 0.002 TYR P 37 PHE 0.019 0.002 PHE O 25 TRP 0.019 0.002 TRP G 913 HIS 0.011 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00319 (39901) covalent geometry : angle 0.62568 (55316) hydrogen bonds : bond 0.04413 ( 1744) hydrogen bonds : angle 4.24459 ( 4841) metal coordination : bond 0.01684 ( 4) metal coordination : angle 11.94652 ( 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 327 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 1.367 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: A 113 MET cc_start: 0.9143 (ttp) cc_final: 0.8842 (ptm) REVERT: A 371 MET cc_start: 0.9523 (mpp) cc_final: 0.8934 (mpp) REVERT: B 20 GLU cc_start: 0.9583 (mm-30) cc_final: 0.9206 (tp30) REVERT: C 61 MET cc_start: 0.8531 (mmt) cc_final: 0.7947 (mmt) REVERT: C 165 LYS cc_start: 0.9405 (tptm) cc_final: 0.9002 (tptp) REVERT: C 178 GLU cc_start: 0.9757 (tt0) cc_final: 0.9308 (mm-30) REVERT: C 260 MET cc_start: 0.9311 (mtm) cc_final: 0.8868 (tpt) REVERT: C 264 MET cc_start: 0.9437 (mmp) cc_final: 0.7900 (mmm) REVERT: C 286 TYR cc_start: 0.9466 (m-80) cc_final: 0.9078 (m-80) REVERT: C 311 CYS cc_start: 0.9282 (m) cc_final: 0.8805 (t) REVERT: C 312 PHE cc_start: 0.9644 (m-80) cc_final: 0.9275 (m-80) REVERT: C 317 ARG cc_start: 0.9302 (tpt170) cc_final: 0.9072 (tpt170) REVERT: C 371 MET cc_start: 0.9333 (mtm) cc_final: 0.8900 (mtp) REVERT: D 46 MET cc_start: 0.9428 (tpt) cc_final: 0.8521 (tpt) REVERT: D 88 MET cc_start: 0.9360 (mmp) cc_final: 0.8904 (mmm) REVERT: D 113 MET cc_start: 0.8655 (ptm) cc_final: 0.7924 (tmm) REVERT: D 303 MET cc_start: 0.8902 (ppp) cc_final: 0.7966 (ttp) REVERT: D 320 MET cc_start: 0.9335 (mmp) cc_final: 0.8846 (mmm) REVERT: D 382 MET cc_start: 0.9372 (tpt) cc_final: 0.9074 (mmm) REVERT: D 442 TYR cc_start: 0.9515 (m-80) cc_final: 0.9235 (m-80) REVERT: D 446 TYR cc_start: 0.9032 (m-80) cc_final: 0.8785 (m-80) REVERT: E 113 MET cc_start: 0.9514 (tpp) cc_final: 0.9256 (tpp) REVERT: E 260 MET cc_start: 0.9525 (tmm) cc_final: 0.9117 (tpt) REVERT: E 264 MET cc_start: 0.8938 (mmp) cc_final: 0.8265 (mmp) REVERT: E 359 MET cc_start: 0.9242 (mpp) cc_final: 0.8950 (mpp) REVERT: E 364 MET cc_start: 0.9071 (pmm) cc_final: 0.8841 (pmm) REVERT: E 371 MET cc_start: 0.9159 (mtp) cc_final: 0.8564 (mtp) REVERT: F 90 MET cc_start: 0.9439 (ttt) cc_final: 0.9168 (tpt) REVERT: F 443 MET cc_start: 0.8315 (ttp) cc_final: 0.7354 (tpp) REVERT: J 91 LYS cc_start: 0.7907 (ptpp) cc_final: 0.7613 (ptpt) REVERT: L 73 ILE cc_start: 0.7989 (mt) cc_final: 0.7508 (tp) REVERT: P 80 LEU cc_start: 0.8611 (mt) cc_final: 0.8018 (mt) outliers start: 1 outliers final: 0 residues processed: 327 average time/residue: 0.2351 time to fit residues: 128.4655 Evaluate side-chains 253 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.666 ------------------------------------------------------------------------------- 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: 50.0000 chunk 305 optimal weight: 2.9990 chunk 287 optimal weight: 4.9990 chunk 225 optimal weight: 1.9990 chunk 268 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 chunk 193 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 466 optimal weight: 30.0000 chunk 448 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 78 GLN ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 GLN D 245 HIS E 115 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 940 HIS ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 49 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.065429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.048119 restraints weight = 410672.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.048612 restraints weight = 265803.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.048205 restraints weight = 200439.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048381 restraints weight = 190079.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.048548 restraints weight = 163674.008| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.8869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 39905 Z= 0.191 Angle : 0.662 21.391 55322 Z= 0.349 Chirality : 0.041 0.213 6487 Planarity : 0.005 0.075 6100 Dihedral : 23.187 123.299 8099 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.23 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -0.03 (0.13), residues: 4393 helix: 0.86 (0.11), residues: 2182 sheet: -0.92 (0.19), residues: 676 loop : -0.73 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 64 TYR 0.044 0.002 TYR P 37 PHE 0.022 0.002 PHE B 209 TRP 0.038 0.003 TRP G 913 HIS 0.010 0.002 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00398 (39901) covalent geometry : angle 0.65140 (55316) hydrogen bonds : bond 0.04902 ( 1744) hydrogen bonds : angle 4.29557 ( 4841) metal coordination : bond 0.01950 ( 4) metal coordination : angle 11.44636 ( 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 312 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.317 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: A 113 MET cc_start: 0.9157 (ttp) cc_final: 0.8851 (ptm) REVERT: A 359 MET cc_start: 0.7792 (mtm) cc_final: 0.7161 (tpp) REVERT: A 371 MET cc_start: 0.9530 (mpp) cc_final: 0.8898 (mpp) REVERT: B 20 GLU cc_start: 0.9581 (mm-30) cc_final: 0.9247 (tp30) REVERT: B 375 CYS cc_start: 0.9346 (m) cc_final: 0.9136 (m) REVERT: C 61 MET cc_start: 0.8555 (mmt) cc_final: 0.8338 (mmt) REVERT: C 165 LYS cc_start: 0.9421 (tptm) cc_final: 0.9047 (tptp) REVERT: C 178 GLU cc_start: 0.9763 (tt0) cc_final: 0.9324 (mm-30) REVERT: C 260 MET cc_start: 0.9295 (mtm) cc_final: 0.8881 (tpt) REVERT: C 264 MET cc_start: 0.9419 (mmp) cc_final: 0.8036 (mmm) REVERT: C 286 TYR cc_start: 0.9475 (m-80) cc_final: 0.9076 (m-80) REVERT: C 311 CYS cc_start: 0.9286 (m) cc_final: 0.8703 (t) REVERT: C 312 PHE cc_start: 0.9654 (m-80) cc_final: 0.9250 (m-10) REVERT: C 316 HIS cc_start: 0.8662 (m90) cc_final: 0.8405 (m90) REVERT: C 371 MET cc_start: 0.9388 (mtm) cc_final: 0.8913 (mtp) REVERT: D 46 MET cc_start: 0.9373 (tpt) cc_final: 0.8468 (tpt) REVERT: D 88 MET cc_start: 0.9395 (mmp) cc_final: 0.8952 (mmm) REVERT: D 113 MET cc_start: 0.8808 (ptm) cc_final: 0.7946 (tmm) REVERT: D 303 MET cc_start: 0.8959 (ppp) cc_final: 0.8027 (ttp) REVERT: D 320 MET cc_start: 0.9359 (mmp) cc_final: 0.8901 (mmm) REVERT: D 442 TYR cc_start: 0.9463 (m-80) cc_final: 0.9183 (m-80) REVERT: D 446 TYR cc_start: 0.9043 (m-80) cc_final: 0.8808 (m-80) REVERT: E 113 MET cc_start: 0.9529 (tpp) cc_final: 0.9276 (tpp) REVERT: E 259 MET cc_start: 0.9665 (ptm) cc_final: 0.9321 (ppp) REVERT: E 260 MET cc_start: 0.9520 (tmm) cc_final: 0.9276 (tmm) REVERT: E 264 MET cc_start: 0.9067 (mmp) cc_final: 0.8500 (mmp) REVERT: E 359 MET cc_start: 0.9256 (mpp) cc_final: 0.8985 (mpp) REVERT: E 364 MET cc_start: 0.9170 (pmm) cc_final: 0.8940 (pmm) REVERT: E 371 MET cc_start: 0.9163 (mtp) cc_final: 0.8612 (mtp) REVERT: F 90 MET cc_start: 0.9440 (ttt) cc_final: 0.9173 (tpt) REVERT: F 218 MET cc_start: 0.8290 (mmp) cc_final: 0.7591 (mmp) REVERT: F 382 MET cc_start: 0.8402 (mmp) cc_final: 0.8116 (mmm) REVERT: F 443 MET cc_start: 0.8325 (ttp) cc_final: 0.7439 (tpp) REVERT: J 91 LYS cc_start: 0.8306 (ptpp) cc_final: 0.7931 (ptpt) REVERT: P 80 LEU cc_start: 0.8765 (mt) cc_final: 0.8497 (mt) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.2321 time to fit residues: 121.6069 Evaluate side-chains 246 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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: 10.0000 chunk 363 optimal weight: 20.0000 chunk 324 optimal weight: 7.9990 chunk 388 optimal weight: 5.9990 chunk 326 optimal weight: 50.0000 chunk 381 optimal weight: 30.0000 chunk 437 optimal weight: 30.0000 chunk 403 optimal weight: 1.9990 chunk 261 optimal weight: 40.0000 chunk 335 optimal weight: 30.0000 chunk 413 optimal weight: 9.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 GLN ** E 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 940 HIS I 76 GLN ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.064552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.047240 restraints weight = 410235.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.047431 restraints weight = 276844.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.047620 restraints weight = 205121.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.047933 restraints weight = 162943.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.047933 restraints weight = 140455.995| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.9342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 39905 Z= 0.221 Angle : 0.696 21.832 55322 Z= 0.368 Chirality : 0.042 0.242 6487 Planarity : 0.005 0.066 6100 Dihedral : 23.313 122.690 8099 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.60 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -0.24 (0.13), residues: 4393 helix: 0.70 (0.11), residues: 2196 sheet: -1.06 (0.19), residues: 685 loop : -0.83 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 416 TYR 0.044 0.002 TYR P 37 PHE 0.018 0.002 PHE G 867 TRP 0.025 0.002 TRP G 913 HIS 0.015 0.002 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00454 (39901) covalent geometry : angle 0.68450 (55316) hydrogen bonds : bond 0.05346 ( 1744) hydrogen bonds : angle 4.43568 ( 4841) metal coordination : bond 0.02192 ( 4) metal coordination : angle 12.01584 ( 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 311 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 1.401 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: A 113 MET cc_start: 0.9149 (ttp) cc_final: 0.8697 (ptm) REVERT: A 359 MET cc_start: 0.7732 (mtm) cc_final: 0.7104 (tpp) REVERT: B 20 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9159 (tp30) REVERT: C 61 MET cc_start: 0.8525 (mmt) cc_final: 0.8316 (mmt) REVERT: C 96 MET cc_start: 0.8164 (tpp) cc_final: 0.7916 (tpp) REVERT: C 165 LYS cc_start: 0.9450 (tptm) cc_final: 0.9090 (tptp) REVERT: C 178 GLU cc_start: 0.9760 (tt0) cc_final: 0.9315 (mm-30) REVERT: C 260 MET cc_start: 0.9259 (mtm) cc_final: 0.8831 (tpt) REVERT: C 264 MET cc_start: 0.9429 (mmp) cc_final: 0.8016 (mmm) REVERT: C 286 TYR cc_start: 0.9538 (m-80) cc_final: 0.9064 (m-80) REVERT: C 311 CYS cc_start: 0.9328 (m) cc_final: 0.8855 (t) REVERT: C 312 PHE cc_start: 0.9650 (m-80) cc_final: 0.9349 (m-80) REVERT: C 316 HIS cc_start: 0.8628 (m90) cc_final: 0.8253 (m90) REVERT: C 371 MET cc_start: 0.9414 (mtm) cc_final: 0.8934 (mtp) REVERT: D 46 MET cc_start: 0.9394 (tpt) cc_final: 0.8819 (tpt) REVERT: D 88 MET cc_start: 0.9359 (mmp) cc_final: 0.8959 (mmm) REVERT: D 113 MET cc_start: 0.8828 (ptm) cc_final: 0.8019 (tmm) REVERT: D 303 MET cc_start: 0.9062 (ppp) cc_final: 0.8222 (ttp) REVERT: D 320 MET cc_start: 0.9379 (mmp) cc_final: 0.8933 (mmm) REVERT: D 446 TYR cc_start: 0.9069 (m-80) cc_final: 0.8759 (m-80) REVERT: E 113 MET cc_start: 0.9546 (tpp) cc_final: 0.9285 (tpp) REVERT: E 259 MET cc_start: 0.9624 (ptm) cc_final: 0.9270 (ppp) REVERT: E 260 MET cc_start: 0.9517 (tmm) cc_final: 0.9179 (tmm) REVERT: E 264 MET cc_start: 0.9071 (mmp) cc_final: 0.8230 (mmp) REVERT: E 359 MET cc_start: 0.9294 (mpp) cc_final: 0.8979 (mpp) REVERT: E 364 MET cc_start: 0.9165 (pmm) cc_final: 0.8905 (pmm) REVERT: E 371 MET cc_start: 0.9118 (mtp) cc_final: 0.8525 (mtp) REVERT: F 90 MET cc_start: 0.9470 (ttt) cc_final: 0.9244 (tpt) REVERT: F 218 MET cc_start: 0.8288 (mmp) cc_final: 0.7558 (mmp) REVERT: F 382 MET cc_start: 0.8565 (mmp) cc_final: 0.8328 (mmm) REVERT: F 443 MET cc_start: 0.8329 (ttp) cc_final: 0.7511 (tpp) REVERT: J 91 LYS cc_start: 0.8344 (ptpp) cc_final: 0.7984 (ptpt) REVERT: N 72 TYR cc_start: 0.7431 (m-80) cc_final: 0.6981 (m-80) REVERT: P 80 LEU cc_start: 0.8737 (mt) cc_final: 0.8413 (mt) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.2328 time to fit residues: 122.2328 Evaluate side-chains 237 residues out of total 3801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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: 20.0000 chunk 249 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 145 optimal weight: 40.0000 chunk 363 optimal weight: 10.0000 chunk 451 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 78 GLN ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 251 ASN ** G 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 940 HIS ** J 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.064941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.046251 restraints weight = 408984.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.046811 restraints weight = 275597.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.047370 restraints weight = 206118.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.047956 restraints weight = 161960.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.048249 restraints weight = 131212.204| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.9513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 39905 Z= 0.187 Angle : 0.654 19.810 55322 Z= 0.345 Chirality : 0.041 0.236 6487 Planarity : 0.004 0.070 6100 Dihedral : 23.243 124.389 8099 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.37 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % 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: -0.11 (0.13), residues: 4393 helix: 0.86 (0.11), residues: 2190 sheet: -1.03 (0.19), residues: 681 loop : -0.84 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 314 TYR 0.061 0.002 TYR P 37 PHE 0.016 0.002 PHE G 867 TRP 0.025 0.002 TRP G 913 HIS 0.010 0.002 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00391 (39901) covalent geometry : angle 0.64387 (55316) hydrogen bonds : bond 0.04769 ( 1744) hydrogen bonds : angle 4.29944 ( 4841) metal coordination : bond 0.01929 ( 4) metal coordination : angle 11.29282 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7175.64 seconds wall clock time: 125 minutes 18.02 seconds (7518.02 seconds total)