Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 18:49:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqf_10550/04_2023/6tqf_10550_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqf_10550/04_2023/6tqf_10550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqf_10550/04_2023/6tqf_10550.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqf_10550/04_2023/6tqf_10550.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqf_10550/04_2023/6tqf_10550_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqf_10550/04_2023/6tqf_10550_updated.pdb" } resolution = 3.5 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 ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 24 5.16 5 C 6718 2.51 5 N 1768 2.21 5 O 1908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 11": "OD1" <-> "OD2" Residue "A ASP 18": "OD1" <-> "OD2" Residue "A TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 110": "OD1" <-> "OD2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A ARG 248": "NH1" <-> "NH2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A ASP 363": "OD1" <-> "OD2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 452": "NH1" <-> "NH2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A ASP 509": "OD1" <-> "OD2" Residue "A ASP 527": "OD1" <-> "OD2" Residue "A ASP 539": "OD1" <-> "OD2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A ASP 546": "OD1" <-> "OD2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A ASP 599": "OD1" <-> "OD2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "B ASP 11": "OD1" <-> "OD2" Residue "B ASP 18": "OD1" <-> "OD2" Residue "B TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B ARG 294": "NH1" <-> "NH2" Residue "B ASP 295": "OD1" <-> "OD2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ASP 363": "OD1" <-> "OD2" Residue "B ASP 366": "OD1" <-> "OD2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 441": "NH1" <-> "NH2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B ARG 461": "NH1" <-> "NH2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "B GLU 492": "OE1" <-> "OE2" Residue "B ASP 509": "OD1" <-> "OD2" Residue "B ASP 527": "OD1" <-> "OD2" Residue "B ASP 539": "OD1" <-> "OD2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B ASP 546": "OD1" <-> "OD2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B ASP 599": "OD1" <-> "OD2" Residue "B GLU 616": "OE1" <-> "OE2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B GLU 633": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10426 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5006 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 603} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5006 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 603} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 207 Unusual residues: {' MG': 1, 'ANP': 1, 'LMT': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 207 Unusual residues: {' MG': 1, 'ANP': 1, 'LMT': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 5.92, per 1000 atoms: 0.57 Number of scatterers: 10426 At special positions: 0 Unit cell: (87.7663, 76.689, 147.413, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 24 16.00 P 6 15.00 Mg 2 11.99 O 1908 8.00 N 1768 7.00 C 6718 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: 3.94 Conformation dependent library (CDL) restraints added in 1.5 seconds 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2348 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 10 sheets defined 34.2% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 21 through 34 removed outlier: 4.150A pdb=" N THR A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 32 " --> pdb=" O THR A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 51 through 54 No H-bonds generated for 'chain 'A' and resid 51 through 54' Processing helix chain 'A' and resid 68 through 71 No H-bonds generated for 'chain 'A' and resid 68 through 71' Processing helix chain 'A' and resid 73 through 101 removed outlier: 3.824A pdb=" N VAL A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 113 through 130 removed outlier: 3.724A pdb=" N ARG A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 removed outlier: 3.758A pdb=" N ASP A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR A 144 " --> pdb=" O MET A 140 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 163 removed outlier: 3.598A pdb=" N TRP A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS A 159 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN A 163 " --> pdb=" O HIS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 Processing helix chain 'A' and resid 220 through 226 removed outlier: 4.520A pdb=" N VAL A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 No H-bonds generated for 'chain 'A' and resid 249 through 252' Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.719A pdb=" N VAL A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 274 through 281 removed outlier: 3.837A pdb=" N ARG A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 274 through 281' Processing helix chain 'A' and resid 288 through 291 No H-bonds generated for 'chain 'A' and resid 288 through 291' Processing helix chain 'A' and resid 297 through 303 removed outlier: 3.677A pdb=" N GLY A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 330 through 333 No H-bonds generated for 'chain 'A' and resid 330 through 333' Processing helix chain 'A' and resid 335 through 342 removed outlier: 3.799A pdb=" N LEU A 339 " --> pdb=" O ASN A 335 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 355 through 358 No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.994A pdb=" N THR A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 381 No H-bonds generated for 'chain 'A' and resid 378 through 381' Processing helix chain 'A' and resid 398 through 408 removed outlier: 3.548A pdb=" N LEU A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 587 through 596 removed outlier: 3.672A pdb=" N GLN A 591 " --> pdb=" O PHE A 587 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A 592 " --> pdb=" O ALA A 588 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 34 removed outlier: 4.150A pdb=" N THR B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 32 " --> pdb=" O THR B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 42 Processing helix chain 'B' and resid 51 through 54 No H-bonds generated for 'chain 'B' and resid 51 through 54' Processing helix chain 'B' and resid 68 through 71 No H-bonds generated for 'chain 'B' and resid 68 through 71' Processing helix chain 'B' and resid 73 through 101 removed outlier: 3.823A pdb=" N VAL B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY B 92 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP B 94 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 113 through 130 removed outlier: 3.724A pdb=" N ARG B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B 123 " --> pdb=" O ARG B 119 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER B 124 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 130 " --> pdb=" O GLY B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 removed outlier: 3.758A pdb=" N ASP B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR B 144 " --> pdb=" O MET B 140 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 146 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 163 removed outlier: 3.599A pdb=" N TRP B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS B 159 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN B 163 " --> pdb=" O HIS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 196 Processing helix chain 'B' and resid 220 through 226 removed outlier: 4.520A pdb=" N VAL B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 252 No H-bonds generated for 'chain 'B' and resid 249 through 252' Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.719A pdb=" N VAL B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 278 through 281 No H-bonds generated for 'chain 'B' and resid 278 through 281' Processing helix chain 'B' and resid 288 through 291 No H-bonds generated for 'chain 'B' and resid 288 through 291' Processing helix chain 'B' and resid 297 through 303 removed outlier: 3.677A pdb=" N GLY B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 330 through 333 No H-bonds generated for 'chain 'B' and resid 330 through 333' Processing helix chain 'B' and resid 335 through 342 removed outlier: 3.798A pdb=" N LEU B 339 " --> pdb=" O ASN B 335 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER B 340 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 350 No H-bonds generated for 'chain 'B' and resid 348 through 350' Processing helix chain 'B' and resid 355 through 358 No H-bonds generated for 'chain 'B' and resid 355 through 358' Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.995A pdb=" N THR B 372 " --> pdb=" O GLY B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 381 No H-bonds generated for 'chain 'B' and resid 378 through 381' Processing helix chain 'B' and resid 398 through 408 removed outlier: 3.548A pdb=" N LEU B 404 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 511 Processing helix chain 'B' and resid 587 through 596 removed outlier: 3.672A pdb=" N GLN B 591 " --> pdb=" O PHE B 587 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU B 592 " --> pdb=" O ALA B 588 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 593 " --> pdb=" O LEU B 589 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 418 through 421 Processing sheet with id= B, first strand: chain 'A' and resid 427 through 429 removed outlier: 3.979A pdb=" N VAL A 427 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 432 through 434 removed outlier: 3.849A pdb=" N GLU A 433 " --> pdb=" O SER A 481 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 455 through 458 removed outlier: 7.008A pdb=" N VAL A 602 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ILE A 458 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N SER A 604 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 617 through 621 Processing sheet with id= F, first strand: chain 'B' and resid 418 through 421 Processing sheet with id= G, first strand: chain 'B' and resid 427 through 429 removed outlier: 3.979A pdb=" N VAL B 427 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 432 through 434 removed outlier: 3.850A pdb=" N GLU B 433 " --> pdb=" O SER B 481 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 455 through 458 removed outlier: 7.009A pdb=" N VAL B 602 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ILE B 458 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N SER B 604 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 617 through 621 142 hydrogen bonds defined for protein. 420 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: 2.37 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3258 1.34 - 1.46: 2303 1.46 - 1.57: 5075 1.57 - 1.69: 10 1.69 - 1.81: 40 Bond restraints: 10686 Sorted by residual: bond pdb=" N3B ANP B 807 " pdb=" PG ANP B 807 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N3B ANP A 807 " pdb=" PG ANP A 807 " ideal model delta sigma weight residual 1.795 1.634 0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" O3A ANP B 807 " pdb=" PB ANP B 807 " ideal model delta sigma weight residual 1.700 1.602 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" O3A ANP A 807 " pdb=" PB ANP A 807 " ideal model delta sigma weight residual 1.700 1.604 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N VAL A 632 " pdb=" CA VAL A 632 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.09e+00 ... (remaining 10681 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.12: 333 107.12 - 113.86: 6204 113.86 - 120.61: 4310 120.61 - 127.35: 3563 127.35 - 134.09: 148 Bond angle restraints: 14558 Sorted by residual: angle pdb=" O GLU A 633 " pdb=" C GLU A 633 " pdb=" N ALA A 634 " ideal model delta sigma weight residual 121.65 125.95 -4.30 8.30e-01 1.45e+00 2.69e+01 angle pdb=" N ILE A 352 " pdb=" CA ILE A 352 " pdb=" C ILE A 352 " ideal model delta sigma weight residual 111.90 108.41 3.49 8.10e-01 1.52e+00 1.85e+01 angle pdb=" N ILE B 352 " pdb=" CA ILE B 352 " pdb=" C ILE B 352 " ideal model delta sigma weight residual 111.90 108.44 3.46 8.10e-01 1.52e+00 1.83e+01 angle pdb=" CA GLU A 633 " pdb=" C GLU A 633 " pdb=" N ALA A 634 " ideal model delta sigma weight residual 119.95 115.24 4.71 1.19e+00 7.06e-01 1.57e+01 angle pdb=" N VAL B 346 " pdb=" CA VAL B 346 " pdb=" C VAL B 346 " ideal model delta sigma weight residual 108.88 117.20 -8.32 2.16e+00 2.14e-01 1.49e+01 ... (remaining 14553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 5364 17.45 - 34.89: 573 34.89 - 52.34: 163 52.34 - 69.78: 26 69.78 - 87.23: 10 Dihedral angle restraints: 6136 sinusoidal: 2486 harmonic: 3650 Sorted by residual: dihedral pdb=" CA LEU A 429 " pdb=" C LEU A 429 " pdb=" N ASN A 430 " pdb=" CA ASN A 430 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LEU B 429 " pdb=" C LEU B 429 " pdb=" N ASN B 430 " pdb=" CA ASN B 430 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA ALA B 464 " pdb=" C ALA B 464 " pdb=" N GLY B 465 " pdb=" CA GLY B 465 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 6133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1283 0.058 - 0.116: 347 0.116 - 0.174: 52 0.174 - 0.232: 8 0.232 - 0.291: 2 Chirality restraints: 1692 Sorted by residual: chirality pdb=" C3' ANP A 807 " pdb=" C2' ANP A 807 " pdb=" C4' ANP A 807 " pdb=" O3' ANP A 807 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C3' ANP B 807 " pdb=" C2' ANP B 807 " pdb=" C4' ANP B 807 " pdb=" O3' ANP B 807 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C1B LMT A 802 " pdb=" C2B LMT A 802 " pdb=" O1B LMT A 802 " pdb=" O5B LMT A 802 " both_signs ideal model delta sigma weight residual False -2.20 -2.40 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1689 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 444 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO A 445 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 444 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO B 445 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 445 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 445 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 354 " 0.035 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO A 355 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.029 5.00e-02 4.00e+02 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 144 2.65 - 3.22: 8333 3.22 - 3.78: 13997 3.78 - 4.34: 19311 4.34 - 4.90: 32470 Nonbonded interactions: 74255 Sorted by model distance: nonbonded pdb=" OG1 THR B 467 " pdb="MG MG B 806 " model vdw 2.092 2.170 nonbonded pdb=" OG1 THR A 467 " pdb="MG MG A 806 " model vdw 2.092 2.170 nonbonded pdb=" OE1 GLN A 498 " pdb="MG MG A 806 " model vdw 2.141 2.170 nonbonded pdb=" OE1 GLN B 498 " pdb="MG MG B 806 " model vdw 2.141 2.170 nonbonded pdb=" O3' LMT A 804 " pdb=" O5B LMT A 804 " model vdw 2.183 2.440 ... (remaining 74250 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 5.620 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 27.950 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.030 ------------------------------------------------------------------------------- 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 : 0.007 0.161 10686 Z= 0.410 Angle : 0.991 11.860 14558 Z= 0.492 Chirality : 0.054 0.291 1692 Planarity : 0.006 0.058 1786 Dihedral : 15.746 87.227 3788 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 0.09 % 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: -6.53 (0.14), residues: 1264 helix: -4.79 (0.07), residues: 722 sheet: -1.47 (0.47), residues: 102 loop : -3.80 (0.20), residues: 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.227 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.3689 time to fit residues: 53.2286 Evaluate side-chains 71 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 338 ASN A 430 ASN B 279 ASN B 338 ASN B 430 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 10686 Z= 0.255 Angle : 0.576 9.294 14558 Z= 0.281 Chirality : 0.041 0.143 1692 Planarity : 0.004 0.035 1786 Dihedral : 9.242 59.395 1524 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 1.04 % 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: -5.71 (0.16), residues: 1264 helix: -4.18 (0.11), residues: 710 sheet: -1.15 (0.50), residues: 102 loop : -3.41 (0.21), residues: 452 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.306 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 89 average time/residue: 0.2782 time to fit residues: 34.6258 Evaluate side-chains 80 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 1.310 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1004 time to fit residues: 2.2611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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: 0.8748 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 10686 Z= 0.331 Angle : 0.601 8.876 14558 Z= 0.293 Chirality : 0.043 0.152 1692 Planarity : 0.004 0.031 1786 Dihedral : 8.753 59.804 1524 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer Outliers : 1.70 % 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: -5.30 (0.18), residues: 1264 helix: -3.78 (0.13), residues: 708 sheet: -0.99 (0.51), residues: 102 loop : -3.36 (0.22), residues: 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 1.249 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 89 average time/residue: 0.2772 time to fit residues: 34.1763 Evaluate side-chains 83 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1097 time to fit residues: 3.9816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 0.0370 chunk 12 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 121 optimal weight: 0.2980 chunk 60 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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: 0.8676 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 10686 Z= 0.124 Angle : 0.499 7.949 14558 Z= 0.242 Chirality : 0.038 0.120 1692 Planarity : 0.003 0.029 1786 Dihedral : 7.907 53.732 1524 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.85 % 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: -4.73 (0.19), residues: 1264 helix: -3.39 (0.15), residues: 702 sheet: -0.32 (0.57), residues: 88 loop : -3.04 (0.23), residues: 474 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 1.262 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 89 average time/residue: 0.2763 time to fit residues: 34.3214 Evaluate side-chains 74 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0955 time to fit residues: 2.0179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 90 optimal weight: 0.0030 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- 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: 0.8728 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 10686 Z= 0.287 Angle : 0.570 8.791 14558 Z= 0.276 Chirality : 0.043 0.139 1692 Planarity : 0.004 0.033 1786 Dihedral : 8.020 55.069 1524 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.85 % 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: -4.66 (0.19), residues: 1264 helix: -3.31 (0.15), residues: 708 sheet: -0.78 (0.51), residues: 102 loop : -2.97 (0.24), residues: 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 1.281 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 83 average time/residue: 0.2822 time to fit residues: 32.4535 Evaluate side-chains 78 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0921 time to fit residues: 2.5871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 117 optimal weight: 0.0170 overall best weight: 0.9022 ------------------------------------------------------------------------------- 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: 0.8688 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 10686 Z= 0.151 Angle : 0.502 8.301 14558 Z= 0.244 Chirality : 0.039 0.121 1692 Planarity : 0.003 0.046 1786 Dihedral : 7.721 55.526 1524 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 0.09 % 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: -4.36 (0.20), residues: 1264 helix: -3.10 (0.16), residues: 714 sheet: -0.22 (0.56), residues: 88 loop : -2.81 (0.24), residues: 462 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 1.376 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.2958 time to fit residues: 32.0435 Evaluate side-chains 71 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.270 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 76 optimal weight: 0.0000 chunk 74 optimal weight: 0.7980 chunk 56 optimal weight: 0.0670 chunk 75 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 overall best weight: 0.4722 ------------------------------------------------------------------------------- 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: 0.8644 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 10686 Z= 0.116 Angle : 0.474 8.161 14558 Z= 0.230 Chirality : 0.038 0.121 1692 Planarity : 0.003 0.030 1786 Dihedral : 7.316 57.985 1524 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 0.38 % 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: -3.92 (0.21), residues: 1264 helix: -2.78 (0.17), residues: 704 sheet: 0.05 (0.56), residues: 86 loop : -2.58 (0.25), residues: 474 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 1.231 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 85 average time/residue: 0.2771 time to fit residues: 32.6848 Evaluate side-chains 73 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 11 optimal weight: 0.0980 chunk 95 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.8635 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 10686 Z= 0.121 Angle : 0.490 7.748 14558 Z= 0.236 Chirality : 0.038 0.121 1692 Planarity : 0.003 0.030 1786 Dihedral : 7.188 58.292 1524 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 0.19 % 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: -3.63 (0.21), residues: 1264 helix: -2.55 (0.17), residues: 718 sheet: 0.17 (0.57), residues: 86 loop : -2.41 (0.26), residues: 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 1.197 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 78 average time/residue: 0.3067 time to fit residues: 32.3846 Evaluate side-chains 75 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 1.276 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1009 time to fit residues: 2.1615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 0.0170 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.3624 ------------------------------------------------------------------------------- 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: 0.8681 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10686 Z= 0.207 Angle : 0.532 8.690 14558 Z= 0.254 Chirality : 0.041 0.119 1692 Planarity : 0.003 0.031 1786 Dihedral : 7.354 57.771 1524 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 0.09 % 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: -3.71 (0.21), residues: 1264 helix: -2.56 (0.17), residues: 722 sheet: -0.46 (0.52), residues: 94 loop : -2.44 (0.26), residues: 448 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.707 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 80 average time/residue: 0.3403 time to fit residues: 36.9618 Evaluate side-chains 79 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 1.265 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1031 time to fit residues: 1.8853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.0010 chunk 56 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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: 0.8648 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 10686 Z= 0.133 Angle : 0.502 7.841 14558 Z= 0.241 Chirality : 0.039 0.122 1692 Planarity : 0.003 0.029 1786 Dihedral : 7.153 58.142 1524 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 0.09 % 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: -3.47 (0.22), residues: 1264 helix: -2.38 (0.18), residues: 720 sheet: 0.09 (0.58), residues: 80 loop : -2.35 (0.26), residues: 464 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.277 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 76 average time/residue: 0.3259 time to fit residues: 33.8351 Evaluate side-chains 72 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0970 time to fit residues: 1.7699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.115989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.087570 restraints weight = 15045.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.090588 restraints weight = 8702.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.092701 restraints weight = 6097.890| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 10686 Z= 0.150 Angle : 0.504 8.331 14558 Z= 0.240 Chirality : 0.039 0.121 1692 Planarity : 0.003 0.029 1786 Dihedral : 7.032 57.755 1524 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.19 % 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: -3.38 (0.22), residues: 1264 helix: -2.30 (0.18), residues: 720 sheet: 0.09 (0.58), residues: 80 loop : -2.32 (0.26), residues: 464 =============================================================================== Job complete usr+sys time: 1866.71 seconds wall clock time: 34 minutes 43.34 seconds (2083.34 seconds total)