Starting phenix.real_space_refine on Wed Feb 14 18:50:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x15_21989/02_2024/6x15_21989_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x15_21989/02_2024/6x15_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x15_21989/02_2024/6x15_21989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x15_21989/02_2024/6x15_21989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x15_21989/02_2024/6x15_21989_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x15_21989/02_2024/6x15_21989_updated.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A ARG 5": "NH1" <-> "NH2" Residue "A GLU 9": "OE1" <-> "OE2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B GLU 9": "OE1" <-> "OE2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 136": "OD1" <-> "OD2" Residue "B ASP 185": "OD1" <-> "OD2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C GLU 9": "OE1" <-> "OE2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C GLU 219": "OE1" <-> "OE2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "A ASP 504": "OD1" <-> "OD2" Residue "B ASP 505": "OD1" <-> "OD2" Residue "C ASP 505": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: 423 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: 423 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: 423 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: 5.75, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 3.95 Conformation dependent library (CDL) restraints added in 1.7 seconds 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... running ksdssp... Secondary structure from input PDB file: 57 helices and 0 sheets defined 76.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 12 through 32 removed outlier: 3.594A pdb=" N LEU A 22 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 42 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 56 removed outlier: 3.810A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 70 removed outlier: 3.814A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 106 Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.877A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 151 through 168 removed outlier: 3.505A pdb=" N PHE A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 220 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 223 through 253 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) Processing helix chain 'A' and resid 258 through 275 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 282 through 291 Processing helix chain 'A' and resid 296 through 309 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 312 through 328 Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.648A pdb=" N VAL A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 370 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) Processing helix chain 'A' and resid 377 through 387 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 390 through 418 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) removed outlier: 3.989A pdb=" N THR A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 8 Processing helix chain 'B' and resid 12 through 32 removed outlier: 3.595A pdb=" N LEU B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 42 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 56 removed outlier: 3.811A pdb=" N PHE B 50 " --> pdb=" O PHE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 70 removed outlier: 3.814A pdb=" N LEU B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 106 Processing helix chain 'B' and resid 130 through 137 removed outlier: 3.878A pdb=" N ILE B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 151 through 168 removed outlier: 3.505A pdb=" N PHE B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 220 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 223 through 253 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) Processing helix chain 'B' and resid 258 through 275 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 282 through 291 Processing helix chain 'B' and resid 296 through 309 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 312 through 328 Processing helix chain 'B' and resid 339 through 351 removed outlier: 3.648A pdb=" N VAL B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 370 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) Processing helix chain 'B' and resid 377 through 387 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 390 through 418 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) removed outlier: 3.989A pdb=" N THR B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 12 through 32 removed outlier: 3.594A pdb=" N LEU C 22 " --> pdb=" O ILE C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 42 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 56 removed outlier: 3.810A pdb=" N PHE C 50 " --> pdb=" O PHE C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 70 removed outlier: 3.813A pdb=" N LEU C 66 " --> pdb=" O VAL C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 106 Processing helix chain 'C' and resid 130 through 137 removed outlier: 3.878A pdb=" N ILE C 137 " --> pdb=" O ILE C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 151 through 168 removed outlier: 3.505A pdb=" N PHE C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 220 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 223 through 253 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) Processing helix chain 'C' and resid 258 through 275 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 282 through 291 Processing helix chain 'C' and resid 296 through 309 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 312 through 328 Processing helix chain 'C' and resid 339 through 351 removed outlier: 3.648A pdb=" N VAL C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 370 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) Processing helix chain 'C' and resid 377 through 387 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 390 through 418 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) removed outlier: 3.989A pdb=" N THR C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1881 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: 2.81 Time building geometry restraints manager: 4.18 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: 100.25 - 106.64: 315 106.64 - 113.02: 5794 113.02 - 119.41: 2715 119.41 - 125.79: 4712 125.79 - 132.18: 90 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 - 34.10: 5808 34.10 - 68.20: 234 68.20 - 102.30: 48 102.30 - 136.40: 18 136.40 - 170.50: 9 Dihedral angle restraints: 6117 sinusoidal: 2547 harmonic: 3570 Sorted by residual: dihedral pdb=" C19 6OU A 507 " pdb=" C20 6OU A 507 " pdb=" C21 6OU A 507 " pdb=" O22 6OU A 507 " ideal model delta sinusoidal sigma weight residual 301.00 130.50 170.50 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C19 6OU B 508 " pdb=" C20 6OU B 508 " pdb=" C21 6OU B 508 " pdb=" O22 6OU B 508 " ideal model delta sinusoidal sigma weight residual 301.00 130.52 170.48 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C19 6OU C 508 " pdb=" C20 6OU C 508 " pdb=" C21 6OU C 508 " pdb=" O22 6OU C 508 " ideal model delta sinusoidal sigma weight residual 301.00 130.52 170.48 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 6114 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: 8990 3.33 - 3.85: 16747 3.85 - 4.38: 19560 4.38 - 4.90: 35035 Nonbonded interactions: 82985 Sorted by model distance: nonbonded pdb=" O ALA C 348 " pdb=" OG1 THR C 352 " model vdw 2.281 2.440 nonbonded pdb=" O ALA A 348 " pdb=" OG1 THR A 352 " model vdw 2.281 2.440 nonbonded pdb=" O ALA B 348 " pdb=" OG1 THR B 352 " model vdw 2.281 2.440 nonbonded pdb=" OG1 THR B 334 " pdb=" O25 6OU B 509 " model vdw 2.301 2.440 nonbonded pdb=" OG1 THR A 334 " pdb=" O25 6OU A 508 " model vdw 2.302 2.440 ... (remaining 82980 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.090 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: 0.000 Extract box with map and model: 4.180 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 29.520 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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= 0.559 Angle : 1.257 15.557 13626 Z= 0.551 Chirality : 0.050 0.244 1638 Planarity : 0.009 0.062 1626 Dihedral : 21.311 170.496 3855 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.003 0.001 HIS C 114 PHE 0.020 0.002 PHE C 323 TYR 0.021 0.002 TYR C 299 ARG 0.002 0.000 ARG A 105 *********************** 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 fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.272 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: 0.8791 (pt) REVERT: B 185 ASP cc_start: 0.8227 (m-30) cc_final: 0.7771 (m-30) REVERT: B 267 ASP cc_start: 0.7680 (m-30) cc_final: 0.7465 (m-30) 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: 0.2698 time to fit residues: 59.2775 Evaluate side-chains 115 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 337 GLN B 121 GLN B 242 GLN B 337 GLN B 338 GLN C 121 GLN C 242 GLN C 337 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10146 Z= 0.196 Angle : 0.532 6.532 13626 Z= 0.269 Chirality : 0.038 0.129 1638 Planarity : 0.005 0.047 1626 Dihedral : 20.712 175.618 1863 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.92 % Allowed : 8.05 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1248 helix: -0.23 (0.16), residues: 1017 sheet: None (None), residues: 0 loop : -1.89 (0.34), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 114 PHE 0.013 0.001 PHE A 323 TYR 0.015 0.001 TYR B 299 ARG 0.003 0.000 ARG A 5 *********************** 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 128 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 1.056 Fit side-chains REVERT: A 95 PHE cc_start: 0.8031 (t80) cc_final: 0.7803 (t80) REVERT: B 59 MET cc_start: 0.8902 (mmm) cc_final: 0.8695 (mmp) REVERT: B 77 ARG cc_start: 0.8316 (ptp-170) cc_final: 0.8061 (ptm160) REVERT: C 22 LEU cc_start: 0.8885 (mt) cc_final: 0.8658 (mt) REVERT: C 136 ASP cc_start: 0.8386 (m-30) cc_final: 0.7857 (m-30) outliers start: 9 outliers final: 8 residues processed: 124 average time/residue: 0.2252 time to fit residues: 39.3952 Evaluate side-chains 124 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 267 ASP Chi-restraints excluded: chain C residue 385 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1667 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= 0.208 Angle : 0.521 6.028 13626 Z= 0.262 Chirality : 0.038 0.125 1638 Planarity : 0.005 0.043 1626 Dihedral : 18.678 179.506 1863 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.12 % Allowed : 9.07 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1248 helix: 0.34 (0.16), residues: 1041 sheet: None (None), residues: 0 loop : -1.60 (0.37), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 125 PHE 0.013 0.001 PHE C 323 TYR 0.016 0.001 TYR C 299 ARG 0.003 0.000 ARG B 5 *********************** 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 131 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.119 Fit side-chains REVERT: A 95 PHE cc_start: 0.8067 (t80) cc_final: 0.7826 (t80) REVERT: A 286 MET cc_start: 0.8527 (mtp) cc_final: 0.8242 (mmm) REVERT: B 185 ASP cc_start: 0.8141 (m-30) cc_final: 0.7812 (m-30) REVERT: C 22 LEU cc_start: 0.8864 (mt) cc_final: 0.8625 (mt) REVERT: C 136 ASP cc_start: 0.8420 (m-30) cc_final: 0.7864 (m-30) REVERT: C 219 GLU cc_start: 0.7163 (tp30) cc_final: 0.6885 (tp30) REVERT: C 220 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7732 (mm-40) outliers start: 11 outliers final: 8 residues processed: 125 average time/residue: 0.2254 time to fit residues: 40.0593 Evaluate side-chains 126 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 140 THR 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 110 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 HIS B 264 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1894 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= 0.221 Angle : 0.519 6.042 13626 Z= 0.261 Chirality : 0.038 0.125 1638 Planarity : 0.004 0.042 1626 Dihedral : 17.500 178.664 1863 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.63 % Allowed : 8.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1248 helix: 0.65 (0.16), residues: 1041 sheet: None (None), residues: 0 loop : -1.22 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 114 PHE 0.015 0.001 PHE A 323 TYR 0.017 0.001 TYR A 299 ARG 0.003 0.000 ARG A 5 *********************** 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 135 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 0.961 Fit side-chains REVERT: A 95 PHE cc_start: 0.8048 (t80) cc_final: 0.7792 (t80) REVERT: A 136 ASP cc_start: 0.8403 (m-30) cc_final: 0.8149 (m-30) REVERT: B 267 ASP cc_start: 0.7680 (m-30) cc_final: 0.7388 (m-30) REVERT: C 22 LEU cc_start: 0.8864 (mt) cc_final: 0.8584 (mt) REVERT: C 136 ASP cc_start: 0.8455 (m-30) cc_final: 0.7908 (m-30) outliers start: 16 outliers final: 10 residues processed: 130 average time/residue: 0.2238 time to fit residues: 41.1314 Evaluate side-chains 127 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 334 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 125 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10146 Z= 0.165 Angle : 0.491 6.005 13626 Z= 0.247 Chirality : 0.037 0.122 1638 Planarity : 0.004 0.041 1626 Dihedral : 16.764 179.857 1863 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.43 % Allowed : 9.79 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.24), residues: 1248 helix: 1.05 (0.17), residues: 1020 sheet: None (None), residues: 0 loop : -1.20 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.009 0.001 PHE A 323 TYR 0.014 0.001 TYR C 299 ARG 0.004 0.000 ARG A 5 *********************** 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 129 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 1.048 Fit side-chains REVERT: A 95 PHE cc_start: 0.8050 (t80) cc_final: 0.7819 (t80) REVERT: B 185 ASP cc_start: 0.8130 (m-30) cc_final: 0.7811 (m-30) REVERT: B 267 ASP cc_start: 0.7637 (m-30) cc_final: 0.7371 (m-30) REVERT: C 22 LEU cc_start: 0.8844 (mt) cc_final: 0.8569 (mt) REVERT: C 136 ASP cc_start: 0.8406 (m-30) cc_final: 0.7872 (m-30) outliers start: 14 outliers final: 12 residues processed: 127 average time/residue: 0.2345 time to fit residues: 41.8196 Evaluate side-chains 124 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 334 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 344 THR 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 107 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2111 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= 0.200 Angle : 0.507 6.112 13626 Z= 0.255 Chirality : 0.038 0.124 1638 Planarity : 0.004 0.040 1626 Dihedral : 16.569 179.118 1863 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.33 % Allowed : 10.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.24), residues: 1248 helix: 1.03 (0.16), residues: 1050 sheet: None (None), residues: 0 loop : -1.13 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 114 PHE 0.012 0.001 PHE A 323 TYR 0.016 0.001 TYR C 299 ARG 0.002 0.000 ARG A 5 *********************** 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 127 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.064 Fit side-chains REVERT: A 95 PHE cc_start: 0.8021 (t80) cc_final: 0.7779 (t80) REVERT: B 267 ASP cc_start: 0.7696 (m-30) cc_final: 0.7427 (m-30) REVERT: C 22 LEU cc_start: 0.8863 (mt) cc_final: 0.8550 (mt) REVERT: C 136 ASP cc_start: 0.8353 (m-30) cc_final: 0.7844 (m-30) outliers start: 13 outliers final: 12 residues processed: 125 average time/residue: 0.2248 time to fit residues: 39.6754 Evaluate side-chains 126 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 334 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 344 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 100 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 54 optimal weight: 0.0040 chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10146 Z= 0.135 Angle : 0.465 5.696 13626 Z= 0.234 Chirality : 0.036 0.122 1638 Planarity : 0.004 0.040 1626 Dihedral : 15.845 179.881 1863 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.24), residues: 1248 helix: 1.32 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -1.01 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.008 0.001 PHE C 210 TYR 0.012 0.001 TYR C 299 ARG 0.002 0.000 ARG C 5 *********************** 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 125 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 0.980 Fit side-chains REVERT: A 95 PHE cc_start: 0.8007 (t80) cc_final: 0.7792 (t80) REVERT: B 185 ASP cc_start: 0.8064 (m-30) cc_final: 0.7711 (m-30) REVERT: B 194 MET cc_start: 0.9241 (mmp) cc_final: 0.8950 (mmp) REVERT: B 220 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7516 (mm-40) REVERT: C 22 LEU cc_start: 0.8840 (mt) cc_final: 0.8578 (mt) REVERT: C 136 ASP cc_start: 0.8274 (m-30) cc_final: 0.7780 (m-30) outliers start: 8 outliers final: 7 residues processed: 124 average time/residue: 0.2205 time to fit residues: 38.8049 Evaluate side-chains 120 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 113 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 344 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 344 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2241 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= 0.198 Angle : 0.496 5.896 13626 Z= 0.251 Chirality : 0.038 0.124 1638 Planarity : 0.004 0.039 1626 Dihedral : 15.829 179.551 1863 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.82 % Allowed : 10.91 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.24), residues: 1248 helix: 1.22 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -1.07 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 114 PHE 0.011 0.001 PHE A 323 TYR 0.015 0.001 TYR C 299 ARG 0.003 0.000 ARG B 77 *********************** 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 121 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 1.100 Fit side-chains REVERT: A 95 PHE cc_start: 0.8009 (t80) cc_final: 0.7776 (t80) REVERT: C 136 ASP cc_start: 0.8264 (m-30) cc_final: 0.7789 (m-30) outliers start: 8 outliers final: 7 residues processed: 119 average time/residue: 0.2267 time to fit residues: 38.2866 Evaluate side-chains 118 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 344 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 0.0050 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 0.3980 chunk 104 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2330 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= 0.149 Angle : 0.471 5.742 13626 Z= 0.237 Chirality : 0.037 0.124 1638 Planarity : 0.004 0.039 1626 Dihedral : 15.309 179.138 1863 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.82 % Allowed : 11.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.24), residues: 1248 helix: 1.39 (0.17), residues: 1035 sheet: None (None), residues: 0 loop : -1.11 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.007 0.001 PHE C 210 TYR 0.013 0.001 TYR C 299 ARG 0.002 0.000 ARG B 77 *********************** 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 119 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 0.942 Fit side-chains REVERT: A 95 PHE cc_start: 0.7986 (t80) cc_final: 0.7759 (t80) REVERT: C 22 LEU cc_start: 0.8801 (mt) cc_final: 0.8446 (mt) REVERT: C 136 ASP cc_start: 0.8239 (m-30) cc_final: 0.7757 (m-30) outliers start: 8 outliers final: 8 residues processed: 118 average time/residue: 0.2263 time to fit residues: 37.6655 Evaluate side-chains 118 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 344 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 0.0570 chunk 10 optimal weight: 0.0370 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10146 Z= 0.134 Angle : 0.458 5.669 13626 Z= 0.230 Chirality : 0.036 0.126 1638 Planarity : 0.004 0.038 1626 Dihedral : 14.691 178.372 1863 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.71 % Allowed : 11.21 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.24), residues: 1248 helix: 1.56 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -0.84 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 114 PHE 0.007 0.001 PHE C 210 TYR 0.012 0.001 TYR C 299 ARG 0.002 0.000 ARG A 5 ********************** 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 124 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 1.067 Fit side-chains REVERT: A 95 PHE cc_start: 0.8031 (t80) cc_final: 0.7745 (t80) REVERT: B 194 MET cc_start: 0.9254 (mmp) cc_final: 0.8946 (mmp) REVERT: C 22 LEU cc_start: 0.8796 (mt) cc_final: 0.8498 (mt) REVERT: C 95 PHE cc_start: 0.8086 (t80) cc_final: 0.7823 (t80) REVERT: C 136 ASP cc_start: 0.8139 (m-30) cc_final: 0.7715 (m-30) outliers start: 7 outliers final: 7 residues processed: 123 average time/residue: 0.2250 time to fit residues: 39.2118 Evaluate side-chains 122 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 334 THR 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 241 LEU Chi-restraints excluded: chain C residue 344 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 chunk 18 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.105229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.087108 restraints weight = 12035.096| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.33 r_work: 0.2751 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10146 Z= 0.148 Angle : 0.464 5.664 13626 Z= 0.234 Chirality : 0.037 0.122 1638 Planarity : 0.004 0.038 1626 Dihedral : 14.650 178.654 1863 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.71 % Allowed : 11.31 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.24), residues: 1248 helix: 1.60 (0.17), residues: 1032 sheet: None (None), residues: 0 loop : -0.75 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.008 0.001 PHE C 210 TYR 0.012 0.001 TYR C 299 ARG 0.003 0.000 ARG B 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2014.05 seconds wall clock time: 37 minutes 22.10 seconds (2242.10 seconds total)