Starting phenix.real_space_refine on Fri Sep 11 16:15:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x15_21989/09_2026/6x15_21989.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x15_21989/09_2026/6x15_21989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x15_21989/09_2026/6x15_21989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x15_21989/09_2026/6x15_21989.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6x15_21989/09_2026/6x15_21989.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x15_21989/09_2026/6x15_21989.cif" model { file = "/net/cci-nas-00/data/ceres_data/6x15_21989/09_2026/6x15_21989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x15_21989/09_2026/6x15_21989.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Hg 3 10.96 5 P 9 5.49 5 S 57 5.16 5 Na 9 4.78 5 C 6705 2.51 5 N 1518 2.21 5 O 1725 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10026 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3112 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 18, 'TRANS': 400} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3112 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 18, 'TRANS': 400} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3112 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 18, 'TRANS': 400} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 227 Unusual residues: {' HG': 1, ' NA': 3, '6OU': 13} Inner-chain residues flagged as termini: ['pdbres="ASP A 504 "'] Classifications: {'peptide': 1, 'undetermined': 17} Modifications used: {'COO': 1} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'6OU:plan-1': 12, '6OU:plan-2': 10, '6OU:plan-3': 10} Unresolved non-hydrogen planarities: 124 Chain: "B" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 227 Unusual residues: {' HG': 1, ' NA': 3, '6OU': 13} Inner-chain residues flagged as termini: ['pdbres="ASP B 505 "'] Classifications: {'peptide': 1, 'undetermined': 17} Modifications used: {'COO': 1} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'6OU:plan-1': 12, '6OU:plan-2': 10, '6OU:plan-3': 10} Unresolved non-hydrogen planarities: 124 Chain: "C" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 227 Unusual residues: {' HG': 1, ' NA': 3, '6OU': 13} Inner-chain residues flagged as termini: ['pdbres="ASP C 505 "'] Classifications: {'peptide': 1, 'undetermined': 17} Modifications used: {'COO': 1} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'6OU:plan-1': 12, '6OU:plan-2': 10, '6OU:plan-3': 10} Unresolved non-hydrogen planarities: 124 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2723 SG CYS A 364 35.989 48.804 29.759 1.00 37.84 S ATOM 5835 SG CYS B 364 60.154 73.323 29.832 1.00 37.84 S ATOM 8947 SG CYS C 364 69.261 40.143 29.721 1.00 37.84 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb="HG HG A 505 " occ=0.30 residue: pdb="HG HG B 506 " occ=0.30 residue: pdb="HG HG C 506 " occ=0.30 Time building chain proxies: 2.53, per 1000 atoms: 0.25 Number of scatterers: 10026 At special positions: 0 Unit cell: (110.292, 111.353, 73.1745, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Hg 3 79.96 S 57 16.00 P 9 15.00 Na 9 11.00 O 1725 8.00 N 1518 7.00 C 6705 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: 0.88 Conformation dependent library (CDL) restraints added in 345.2 milliseconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2262 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 0 sheets defined 83.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 3.911A pdb=" N ARG A 5 " --> pdb=" O FME A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 33 removed outlier: 3.594A pdb=" N LEU A 22 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 removed outlier: 3.764A pdb=" N VAL A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.810A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 71 removed outlier: 3.673A pdb=" N ILE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 107 removed outlier: 3.713A pdb=" N LYS A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 150 through 169 removed outlier: 3.523A pdb=" N THR A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 removed outlier: 3.825A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.724A pdb=" N TYR A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 254 removed outlier: 4.230A pdb=" N GLY A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 5.603A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.661A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 4.247A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 329 Processing helix chain 'A' and resid 338 through 352 removed outlier: 3.664A pdb=" N VAL A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 371 removed outlier: 3.562A pdb=" N MET A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 388 removed outlier: 3.611A pdb=" N ALA A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 417 removed outlier: 3.642A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 Processing helix chain 'B' and resid 11 through 33 removed outlier: 3.595A pdb=" N LEU B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 43 removed outlier: 3.764A pdb=" N VAL B 39 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.811A pdb=" N PHE B 50 " --> pdb=" O PHE B 46 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 71 removed outlier: 3.673A pdb=" N ILE B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 107 removed outlier: 3.713A pdb=" N LYS B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 136 Processing helix chain 'B' and resid 141 through 148 Processing helix chain 'B' and resid 150 through 169 removed outlier: 3.523A pdb=" N THR B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 221 removed outlier: 3.826A pdb=" N GLN B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) Proline residue: B 206 - end of helix removed outlier: 3.724A pdb=" N TYR B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 254 removed outlier: 4.230A pdb=" N GLY B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 230 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 5.604A pdb=" N ASP B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ALA B 268 " --> pdb=" O HIS B 264 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 295 through 310 removed outlier: 4.661A pdb=" N PHE B 301 " --> pdb=" O GLY B 297 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 303 " --> pdb=" O TYR B 299 " (cutoff:3.500A) Proline residue: B 304 - end of helix removed outlier: 4.247A pdb=" N THR B 308 " --> pdb=" O PRO B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 329 Processing helix chain 'B' and resid 338 through 352 removed outlier: 3.664A pdb=" N VAL B 342 " --> pdb=" O GLN B 338 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 371 removed outlier: 3.562A pdb=" N MET B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET B 365 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 366 " --> pdb=" O MET B 362 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 370 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 388 removed outlier: 3.611A pdb=" N ALA B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 417 removed outlier: 3.643A pdb=" N LEU B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N MET B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 11 through 33 removed outlier: 3.594A pdb=" N LEU C 22 " --> pdb=" O ILE C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.764A pdb=" N VAL C 39 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 57 removed outlier: 3.810A pdb=" N PHE C 50 " --> pdb=" O PHE C 46 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 71 removed outlier: 3.673A pdb=" N ILE C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 66 " --> pdb=" O VAL C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 107 removed outlier: 3.714A pdb=" N LYS C 84 " --> pdb=" O ARG C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 150 through 169 removed outlier: 3.523A pdb=" N THR C 154 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 221 removed outlier: 3.825A pdb=" N GLN C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) Proline residue: C 206 - end of helix removed outlier: 3.724A pdb=" N TYR C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 254 removed outlier: 4.230A pdb=" N GLY C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS C 230 " --> pdb=" O GLY C 226 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 276 removed outlier: 5.604A pdb=" N ASP C 267 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ALA C 268 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 295 through 310 removed outlier: 4.661A pdb=" N PHE C 301 " --> pdb=" O GLY C 297 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C 303 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Proline residue: C 304 - end of helix removed outlier: 4.247A pdb=" N THR C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 329 Processing helix chain 'C' and resid 338 through 352 removed outlier: 3.664A pdb=" N VAL C 342 " --> pdb=" O GLN C 338 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.562A pdb=" N MET C 362 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N MET C 365 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 366 " --> pdb=" O MET C 362 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 388 removed outlier: 3.612A pdb=" N ALA C 384 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 417 removed outlier: 3.643A pdb=" N LEU C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N MET C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) 696 hydrogen bonds defined for protein. 2088 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1479 1.31 - 1.43: 2368 1.43 - 1.55: 6057 1.55 - 1.68: 134 1.68 - 1.80: 108 Bond restraints: 10146 Sorted by residual: bond pdb=" C16 6OU B 509 " pdb=" O18 6OU B 509 " ideal model delta sigma weight residual 1.327 1.419 -0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C16 6OU C 509 " pdb=" O18 6OU C 509 " ideal model delta sigma weight residual 1.327 1.419 -0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C16 6OU A 508 " pdb=" O18 6OU A 508 " ideal model delta sigma weight residual 1.327 1.419 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C16 6OU C 508 " pdb=" O18 6OU C 508 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" C16 6OU A 507 " pdb=" O18 6OU A 507 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 1.96e+01 ... (remaining 10141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 13033 3.11 - 6.22: 527 6.22 - 9.33: 42 9.33 - 12.45: 15 12.45 - 15.56: 9 Bond angle restraints: 13626 Sorted by residual: angle pdb=" O22 6OU B 508 " pdb=" P23 6OU B 508 " pdb=" O26 6OU B 508 " ideal model delta sigma weight residual 93.95 109.51 -15.56 3.00e+00 1.11e-01 2.69e+01 angle pdb=" O22 6OU A 507 " pdb=" P23 6OU A 507 " pdb=" O26 6OU A 507 " ideal model delta sigma weight residual 93.95 109.48 -15.53 3.00e+00 1.11e-01 2.68e+01 angle pdb=" O22 6OU C 508 " pdb=" P23 6OU C 508 " pdb=" O26 6OU C 508 " ideal model delta sigma weight residual 93.95 109.47 -15.52 3.00e+00 1.11e-01 2.68e+01 angle pdb=" O22 6OU A 508 " pdb=" P23 6OU A 508 " pdb=" O26 6OU A 508 " ideal model delta sigma weight residual 93.95 109.30 -15.35 3.00e+00 1.11e-01 2.62e+01 angle pdb=" O22 6OU C 509 " pdb=" P23 6OU C 509 " pdb=" O26 6OU C 509 " ideal model delta sigma weight residual 93.95 109.25 -15.30 3.00e+00 1.11e-01 2.60e+01 ... (remaining 13621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.50: 5694 28.50 - 57.00: 255 57.00 - 85.50: 36 85.50 - 114.00: 15 114.00 - 142.50: 18 Dihedral angle restraints: 6018 sinusoidal: 2448 harmonic: 3570 Sorted by residual: dihedral pdb=" C13 6OU B 509 " pdb=" C14 6OU B 509 " pdb=" C15 6OU B 509 " pdb=" C16 6OU B 509 " ideal model delta sinusoidal sigma weight residual -169.65 -27.15 -142.50 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C13 6OU C 509 " pdb=" C14 6OU C 509 " pdb=" C15 6OU C 509 " pdb=" C16 6OU C 509 " ideal model delta sinusoidal sigma weight residual -169.65 -27.18 -142.47 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C13 6OU A 508 " pdb=" C14 6OU A 508 " pdb=" C15 6OU A 508 " pdb=" C16 6OU A 508 " ideal model delta sinusoidal sigma weight residual -169.65 -27.19 -142.46 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 6015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1187 0.049 - 0.098: 349 0.098 - 0.146: 81 0.146 - 0.195: 13 0.195 - 0.244: 8 Chirality restraints: 1638 Sorted by residual: chirality pdb=" C20 6OU C 509 " pdb=" C19 6OU C 509 " pdb=" C21 6OU C 509 " pdb=" O30 6OU C 509 " both_signs ideal model delta sigma weight residual False 2.35 2.59 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C20 6OU B 509 " pdb=" C19 6OU B 509 " pdb=" C21 6OU B 509 " pdb=" O30 6OU B 509 " both_signs ideal model delta sigma weight residual False 2.35 2.59 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C20 6OU A 508 " pdb=" C19 6OU A 508 " pdb=" C21 6OU A 508 " pdb=" O30 6OU A 508 " both_signs ideal model delta sigma weight residual False 2.35 2.59 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1635 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 44 " 0.042 5.00e-02 4.00e+02 6.24e-02 6.22e+00 pdb=" N PRO C 45 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 45 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 45 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.042 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO A 45 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 44 " -0.042 5.00e-02 4.00e+02 6.22e-02 6.18e+00 pdb=" N PRO B 45 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 45 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 45 " -0.035 5.00e-02 4.00e+02 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2653 2.80 - 3.33: 8942 3.33 - 3.85: 16672 3.85 - 4.38: 19443 4.38 - 4.90: 34999 Nonbonded interactions: 82709 Sorted by model distance: nonbonded pdb=" O ALA C 348 " pdb=" OG1 THR C 352 " model vdw 2.281 3.040 nonbonded pdb=" O ALA A 348 " pdb=" OG1 THR A 352 " model vdw 2.281 3.040 nonbonded pdb=" O ALA B 348 " pdb=" OG1 THR B 352 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR B 334 " pdb=" O25 6OU B 509 " model vdw 2.301 3.040 nonbonded pdb=" OG1 THR A 334 " pdb=" O25 6OU A 508 " model vdw 2.302 3.040 ... (remaining 82704 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 419 or resid 502 through 503 or resid 507 throug \ h 508 or resid 510 through 514 or (resid 515 through 518 and (name C01 or name C \ 02 or name C03 or name C04 or name C05 or name C06)))) selection = (chain 'B' and (resid 1 through 419 or resid 502 through 503 or (resid 507 and ( \ name C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 \ or name C08 or name C09 or name C10 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C19 or name C20 or name C21 or name C27 or \ name C28 or name C31 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name N29 or name O17 or name O18 or name \ O22 or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)) o \ r (resid 508 and (name C10 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C16 or name C19 or name C20 or name C21 or name C27 or name C28 o \ r name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name N29 or name O17 or name O18 or name O22 or name O24 or name O25 or na \ me O26 or name O30 or name O32 or name P23)) or (resid 510 through 511 and (name \ C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or \ name C08 or name C09 or name C10 or name C11 or name C12)) or (resid 512 and (na \ me C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 o \ r name C08 or name C09 or name C10)) or (resid 513 through 518 and (name C01 or \ name C02 or name C03 or name C04 or name C05 or name C06)))) selection = (chain 'C' and (resid 1 through 419 or resid 502 through 503 or (resid 507 and ( \ name C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 \ or name C08 or name C09 or name C10 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C19 or name C20 or name C21 or name C27 or \ name C28 or name C31 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name N29 or name O17 or name O18 or name \ O22 or name O24 or name O25 or name O26 or name O30 or name O32 or name P23)) o \ r (resid 508 and (name C10 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C16 or name C19 or name C20 or name C21 or name C27 or name C28 o \ r name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name N29 or name O17 or name O18 or name O22 or name O24 or name O25 or na \ me O26 or name O30 or name O32 or name P23)) or (resid 510 through 511 and (name \ C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or \ name C08 or name C09 or name C10 or name C11 or name C12)) or (resid 512 and (na \ me C01 or name C02 or name C03 or name C04 or name C05 or name C06 or name C07 o \ r name C08 or name C09 or name C10)) or (resid 513 through 518 and (name C01 or \ name C02 or name C03 or name C04 or name C05 or name C06)))) } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.220 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 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 : 0.009 0.092 10146 Z= 0.418 Angle : 1.257 15.557 13626 Z= 0.551 Chirality : 0.050 0.244 1638 Planarity : 0.009 0.062 1626 Dihedral : 19.041 142.502 3756 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.17), residues: 1248 helix: -2.29 (0.11), residues: 1029 sheet: None (None), residues: 0 loop : -2.37 (0.33), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 105 TYR 0.021 0.002 TYR C 299 PHE 0.020 0.002 PHE C 323 HIS 0.003 0.001 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00863 / 0.42 (10146) covalent geometry : angle 1.25681 / 0.55 (13626) hydrogen bonds : bond 0.13418 / 9.19 ( 696) hydrogen bonds : angle 6.30888 / 4.42 ( 2088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.285 Fit side-chains REVERT: A 95 PHE cc_start: 0.8070 (t80) cc_final: 0.7831 (t80) REVERT: A 132 HIS cc_start: 0.7939 (m90) cc_final: 0.7641 (m-70) REVERT: A 136 ASP cc_start: 0.8316 (m-30) cc_final: 0.8115 (m-30) REVERT: A 202 MET cc_start: 0.9219 (mmm) cc_final: 0.8987 (mmp) REVERT: B 18 ILE cc_start: 0.9086 (pt) cc_final: 0.8792 (pt) REVERT: B 185 ASP cc_start: 0.8227 (m-30) cc_final: 0.7770 (m-30) REVERT: B 267 ASP cc_start: 0.7681 (m-30) cc_final: 0.7466 (m-30) REVERT: C 22 LEU cc_start: 0.8925 (mt) cc_final: 0.8650 (mt) REVERT: C 136 ASP cc_start: 0.8314 (m-30) cc_final: 0.8036 (m-30) REVERT: C 194 MET cc_start: 0.9080 (mmm) cc_final: 0.8861 (mmp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1173 time to fit residues: 26.0575 Evaluate side-chains 116 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 GLN A 337 GLN B 121 GLN B 242 GLN B 337 GLN C 121 GLN C 242 GLN C 337 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.103432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.085225 restraints weight = 12178.853| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 1.33 r_work: 0.2725 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10146 Z= 0.132 Angle : 0.541 6.422 13626 Z= 0.278 Chirality : 0.038 0.130 1638 Planarity : 0.005 0.047 1626 Dihedral : 17.522 125.743 1764 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.82 % Allowed : 8.46 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.22), residues: 1248 helix: -0.20 (0.15), residues: 1053 sheet: None (None), residues: 0 loop : -2.47 (0.33), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 5 TYR 0.025 0.001 TYR B 299 PHE 0.013 0.001 PHE A 323 HIS 0.002 0.001 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10146) covalent geometry : angle 0.54103 / 0.28 (13626) hydrogen bonds : bond 0.04594 / 3.07 ( 696) hydrogen bonds : angle 4.36863 / 3.09 ( 2088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.380 Fit side-chains REVERT: A 95 PHE cc_start: 0.8327 (t80) cc_final: 0.8099 (t80) REVERT: A 136 ASP cc_start: 0.8627 (m-30) cc_final: 0.8415 (m-30) REVERT: B 56 MET cc_start: 0.9277 (ttp) cc_final: 0.9075 (ttp) REVERT: B 59 MET cc_start: 0.9071 (mmm) cc_final: 0.8858 (mmp) REVERT: B 136 ASP cc_start: 0.8810 (m-30) cc_final: 0.8534 (m-30) REVERT: C 136 ASP cc_start: 0.8772 (m-30) cc_final: 0.8180 (m-30) outliers start: 8 outliers final: 5 residues processed: 136 average time/residue: 0.0941 time to fit residues: 18.4792 Evaluate side-chains 119 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 267 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 52 optimal weight: 0.0970 chunk 95 optimal weight: 0.0870 chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS A 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.104540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.086500 restraints weight = 12619.024| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.37 r_work: 0.2760 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10146 Z= 0.108 Angle : 0.501 6.385 13626 Z= 0.253 Chirality : 0.037 0.124 1638 Planarity : 0.005 0.043 1626 Dihedral : 15.218 119.619 1764 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.61 % Allowed : 9.38 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.24), residues: 1248 helix: 0.56 (0.16), residues: 1059 sheet: None (None), residues: 0 loop : -1.87 (0.38), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 5 TYR 0.020 0.001 TYR B 299 PHE 0.009 0.001 PHE C 323 HIS 0.001 0.000 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (10146) covalent geometry : angle 0.50068 / 0.25 (13626) hydrogen bonds : bond 0.03851 / 2.57 ( 696) hydrogen bonds : angle 4.06499 / 2.87 ( 2088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.327 Fit side-chains REVERT: B 136 ASP cc_start: 0.8688 (m-30) cc_final: 0.8427 (m-30) REVERT: C 136 ASP cc_start: 0.8664 (m-30) cc_final: 0.8103 (m-30) outliers start: 6 outliers final: 5 residues processed: 125 average time/residue: 0.0955 time to fit residues: 17.2085 Evaluate side-chains 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain C residue 241 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 93 optimal weight: 0.0770 chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 0.0170 chunk 73 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.105534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.087629 restraints weight = 12614.794| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.36 r_work: 0.2772 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10146 Z= 0.099 Angle : 0.481 5.772 13626 Z= 0.244 Chirality : 0.037 0.122 1638 Planarity : 0.004 0.042 1626 Dihedral : 14.237 112.753 1764 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.02 % Allowed : 9.58 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.24), residues: 1248 helix: 0.99 (0.16), residues: 1053 sheet: None (None), residues: 0 loop : -1.56 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 5 TYR 0.019 0.001 TYR B 299 PHE 0.010 0.001 PHE C 95 HIS 0.001 0.000 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (10146) covalent geometry : angle 0.48143 / 0.24 (13626) hydrogen bonds : bond 0.03548 / 2.37 ( 696) hydrogen bonds : angle 3.92357 / 2.77 ( 2088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.351 Fit side-chains REVERT: A 365 MET cc_start: 0.8758 (ptm) cc_final: 0.8127 (ptm) REVERT: B 136 ASP cc_start: 0.8697 (m-30) cc_final: 0.8462 (m-30) REVERT: B 224 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.8089 (m) REVERT: C 136 ASP cc_start: 0.8634 (m-30) cc_final: 0.8108 (m-30) outliers start: 10 outliers final: 7 residues processed: 138 average time/residue: 0.0931 time to fit residues: 18.5846 Evaluate side-chains 127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 241 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.102600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.084540 restraints weight = 12675.135| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.37 r_work: 0.2723 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10146 Z= 0.124 Angle : 0.506 5.893 13626 Z= 0.256 Chirality : 0.038 0.125 1638 Planarity : 0.004 0.039 1626 Dihedral : 13.650 102.900 1764 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.82 % Allowed : 10.60 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1248 helix: 1.25 (0.16), residues: 1035 sheet: None (None), residues: 0 loop : -1.49 (0.38), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 5 TYR 0.021 0.001 TYR C 299 PHE 0.012 0.001 PHE A 323 HIS 0.002 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (10146) covalent geometry : angle 0.50593 / 0.26 (13626) hydrogen bonds : bond 0.04112 / 2.74 ( 696) hydrogen bonds : angle 4.00714 / 2.83 ( 2088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.354 Fit side-chains REVERT: B 136 ASP cc_start: 0.8678 (m-30) cc_final: 0.8435 (m-30) REVERT: C 136 ASP cc_start: 0.8616 (m-30) cc_final: 0.8098 (m-30) outliers start: 8 outliers final: 7 residues processed: 129 average time/residue: 0.0972 time to fit residues: 17.9482 Evaluate side-chains 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 118 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.101568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.083520 restraints weight = 12825.142| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.37 r_work: 0.2678 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2566 r_free = 0.2566 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10146 Z= 0.131 Angle : 0.510 5.925 13626 Z= 0.259 Chirality : 0.038 0.125 1638 Planarity : 0.004 0.040 1626 Dihedral : 13.310 97.827 1764 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.02 % Allowed : 10.81 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.24), residues: 1248 helix: 1.27 (0.16), residues: 1053 sheet: None (None), residues: 0 loop : -1.76 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 5 TYR 0.021 0.001 TYR C 299 PHE 0.012 0.001 PHE A 323 HIS 0.002 0.001 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (10146) covalent geometry : angle 0.51039 / 0.26 (13626) hydrogen bonds : bond 0.04225 / 2.81 ( 696) hydrogen bonds : angle 4.04636 / 2.86 ( 2088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.382 Fit side-chains REVERT: B 136 ASP cc_start: 0.8697 (m-30) cc_final: 0.8468 (m-30) REVERT: C 136 ASP cc_start: 0.8631 (m-30) cc_final: 0.8143 (m-30) outliers start: 10 outliers final: 9 residues processed: 127 average time/residue: 0.0987 time to fit residues: 18.1123 Evaluate side-chains 127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 GLN B 264 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.100016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.081865 restraints weight = 12819.849| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 1.37 r_work: 0.2677 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10146 Z= 0.162 Angle : 0.540 6.005 13626 Z= 0.275 Chirality : 0.039 0.123 1638 Planarity : 0.004 0.040 1626 Dihedral : 13.400 98.157 1764 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.22 % Allowed : 11.21 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.24), residues: 1248 helix: 1.23 (0.16), residues: 1053 sheet: None (None), residues: 0 loop : -1.74 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 5 TYR 0.022 0.001 TYR B 299 PHE 0.014 0.001 PHE C 323 HIS 0.002 0.001 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (10146) covalent geometry : angle 0.54018 / 0.27 (13626) hydrogen bonds : bond 0.04667 / 3.11 ( 696) hydrogen bonds : angle 4.12804 / 2.92 ( 2088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.426 Fit side-chains REVERT: A 95 PHE cc_start: 0.8356 (t80) cc_final: 0.8150 (t80) REVERT: C 136 ASP cc_start: 0.8680 (m-30) cc_final: 0.8208 (m-30) outliers start: 12 outliers final: 8 residues processed: 128 average time/residue: 0.1012 time to fit residues: 18.4149 Evaluate side-chains 121 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 106 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.102135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.084163 restraints weight = 12735.482| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.36 r_work: 0.2719 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10146 Z= 0.119 Angle : 0.500 5.932 13626 Z= 0.255 Chirality : 0.038 0.123 1638 Planarity : 0.004 0.040 1626 Dihedral : 12.958 97.750 1764 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.12 % Allowed : 11.31 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.24), residues: 1248 helix: 1.41 (0.16), residues: 1050 sheet: None (None), residues: 0 loop : -1.62 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 5 TYR 0.019 0.001 TYR C 299 PHE 0.008 0.001 PHE C 323 HIS 0.002 0.000 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (10146) covalent geometry : angle 0.50007 / 0.26 (13626) hydrogen bonds : bond 0.04017 / 2.67 ( 696) hydrogen bonds : angle 4.02921 / 2.85 ( 2088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.376 Fit side-chains REVERT: A 95 PHE cc_start: 0.8305 (t80) cc_final: 0.8080 (t80) REVERT: A 338 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8535 (mt0) REVERT: B 185 ASP cc_start: 0.8754 (m-30) cc_final: 0.8437 (m-30) REVERT: C 136 ASP cc_start: 0.8630 (m-30) cc_final: 0.8165 (m-30) outliers start: 11 outliers final: 8 residues processed: 127 average time/residue: 0.1000 time to fit residues: 18.2707 Evaluate side-chains 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 0.0970 chunk 113 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.101095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.083122 restraints weight = 12735.978| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.36 r_work: 0.2697 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10146 Z= 0.138 Angle : 0.518 5.980 13626 Z= 0.264 Chirality : 0.038 0.124 1638 Planarity : 0.004 0.040 1626 Dihedral : 12.951 97.476 1764 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.02 % Allowed : 11.52 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.24), residues: 1248 helix: 1.35 (0.16), residues: 1053 sheet: None (None), residues: 0 loop : -1.54 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 5 TYR 0.021 0.001 TYR C 299 PHE 0.011 0.001 PHE C 323 HIS 0.002 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (10146) covalent geometry : angle 0.51812 / 0.26 (13626) hydrogen bonds : bond 0.04316 / 2.87 ( 696) hydrogen bonds : angle 4.07617 / 2.88 ( 2088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.353 Fit side-chains REVERT: A 95 PHE cc_start: 0.8282 (t80) cc_final: 0.8030 (t80) REVERT: C 136 ASP cc_start: 0.8617 (m-30) cc_final: 0.8144 (m-30) outliers start: 10 outliers final: 9 residues processed: 126 average time/residue: 0.0992 time to fit residues: 18.0127 Evaluate side-chains 126 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.102465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.084559 restraints weight = 12621.539| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 1.36 r_work: 0.2722 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10146 Z= 0.118 Angle : 0.496 5.905 13626 Z= 0.254 Chirality : 0.038 0.122 1638 Planarity : 0.004 0.040 1626 Dihedral : 12.598 97.103 1764 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.82 % Allowed : 11.72 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.24), residues: 1248 helix: 1.48 (0.16), residues: 1047 sheet: None (None), residues: 0 loop : -1.32 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 5 TYR 0.019 0.001 TYR A 299 PHE 0.008 0.001 PHE C 323 HIS 0.002 0.000 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10146) covalent geometry : angle 0.49634 / 0.25 (13626) hydrogen bonds : bond 0.03961 / 2.63 ( 696) hydrogen bonds : angle 4.01354 / 2.84 ( 2088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.401 Fit side-chains REVERT: A 95 PHE cc_start: 0.8308 (t80) cc_final: 0.8048 (t80) REVERT: B 194 MET cc_start: 0.9421 (mmp) cc_final: 0.9089 (mmp) REVERT: C 136 ASP cc_start: 0.8605 (m-30) cc_final: 0.8130 (m-30) outliers start: 8 outliers final: 8 residues processed: 123 average time/residue: 0.1012 time to fit residues: 17.9867 Evaluate side-chains 123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 241 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 87 optimal weight: 0.1980 chunk 20 optimal weight: 0.0020 chunk 63 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.086055 restraints weight = 12760.388| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.37 r_work: 0.2747 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (31 function evaluations) r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10146 Z= 0.107 Angle : 0.482 5.802 13626 Z= 0.246 Chirality : 0.037 0.122 1638 Planarity : 0.004 0.040 1626 Dihedral : 12.163 95.828 1764 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.92 % Allowed : 12.03 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.24), residues: 1248 helix: 1.56 (0.16), residues: 1047 sheet: None (None), residues: 0 loop : -1.19 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 5 TYR 0.018 0.001 TYR C 299 PHE 0.008 0.001 PHE C 210 HIS 0.001 0.000 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (10146) covalent geometry : angle 0.48180 / 0.25 (13626) hydrogen bonds : bond 0.03671 / 2.43 ( 696) hydrogen bonds : angle 3.94343 / 2.79 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2284.11 seconds wall clock time: 39 minutes 54.38 seconds (2394.38 seconds total)