Starting phenix.real_space_refine on Fri Mar 15 02:51:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqf_10550/03_2024/6tqf_10550_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqf_10550/03_2024/6tqf_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_10550/03_2024/6tqf_10550.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqf_10550/03_2024/6tqf_10550.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqf_10550/03_2024/6tqf_10550_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqf_10550/03_2024/6tqf_10550_updated.pdb" } resolution = 3.5 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= 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-dev-5265/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: 6.08, per 1000 atoms: 0.58 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: 3.69 Conformation dependent library (CDL) restraints added in 1.9 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: 2.80 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: 2.55 Time building geometry restraints manager: 4.00 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 - 26.39: 6092 26.39 - 52.78: 447 52.78 - 79.17: 62 79.17 - 105.56: 71 105.56 - 131.95: 20 Dihedral angle restraints: 6692 sinusoidal: 3042 harmonic: 3650 Sorted by residual: dihedral pdb=" C2B LMT A 801 " pdb=" C1B LMT A 801 " pdb=" O5B LMT A 801 " pdb=" C5B LMT A 801 " ideal model delta sinusoidal sigma weight residual -57.12 74.83 -131.95 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C2B LMT B 805 " pdb=" C1B LMT B 805 " pdb=" O5B LMT B 805 " pdb=" C5B LMT B 805 " ideal model delta sinusoidal sigma weight residual -57.12 74.78 -131.90 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C5B LMT B 805 " pdb=" C1B LMT B 805 " pdb=" O5B LMT B 805 " pdb=" O1B LMT B 805 " ideal model delta sinusoidal sigma weight residual 295.61 163.78 131.83 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 6689 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: 0.900 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: 5.150 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 30.370 Find NCS groups from input model: 0.510 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.900 ------------------------------------------------------------------------------- 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 : 22.161 131.947 4344 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 % Allowed : 8.60 % Favored : 91.30 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 477 HIS 0.003 0.001 HIS B 378 PHE 0.018 0.001 PHE A 317 TYR 0.008 0.001 TYR B 21 ARG 0.003 0.000 ARG A 270 *********************** 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 : 0.932 Fit side-chains REVERT: A 80 LEU cc_start: 0.9236 (tp) cc_final: 0.9034 (tp) REVERT: A 164 ASP cc_start: 0.8450 (t70) cc_final: 0.8105 (t0) REVERT: A 543 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7237 (mt-10) REVERT: B 543 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7236 (mt-10) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.3497 time to fit residues: 50.1284 Evaluate side-chains 74 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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: 0.8716 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10686 Z= 0.262 Angle : 0.684 9.238 14558 Z= 0.305 Chirality : 0.049 0.438 1692 Planarity : 0.004 0.037 1786 Dihedral : 13.138 83.876 2080 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.13 % Allowed : 14.56 % Favored : 84.31 % 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: -5.69 (0.17), residues: 1264 helix: -4.15 (0.11), residues: 728 sheet: -1.16 (0.50), residues: 102 loop : -3.34 (0.22), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 477 HIS 0.002 0.001 HIS A 135 PHE 0.014 0.001 PHE B 573 TYR 0.007 0.001 TYR A 96 ARG 0.003 0.000 ARG A 486 *********************** 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 92 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 1.233 Fit side-chains REVERT: A 543 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6949 (mt-10) REVERT: B 543 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7010 (mt-10) outliers start: 12 outliers final: 4 residues processed: 90 average time/residue: 0.2710 time to fit residues: 33.7920 Evaluate side-chains 79 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 129 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 0.1980 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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: 0.8713 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10686 Z= 0.232 Angle : 0.590 8.445 14558 Z= 0.275 Chirality : 0.045 0.368 1692 Planarity : 0.004 0.031 1786 Dihedral : 10.712 88.283 2080 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.70 % Allowed : 16.73 % Favored : 81.57 % 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: -5.16 (0.18), residues: 1264 helix: -3.71 (0.14), residues: 716 sheet: -0.85 (0.51), residues: 102 loop : -3.21 (0.23), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 477 HIS 0.002 0.001 HIS B 402 PHE 0.012 0.001 PHE A 573 TYR 0.007 0.001 TYR A 21 ARG 0.003 0.000 ARG A 66 *********************** 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 97 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 1.148 Fit side-chains REVERT: A 166 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8438 (pp) REVERT: A 543 GLU cc_start: 0.7473 (mt-10) cc_final: 0.6956 (mt-10) REVERT: B 166 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8436 (pp) REVERT: B 543 GLU cc_start: 0.7524 (mt-10) cc_final: 0.6956 (mt-10) outliers start: 18 outliers final: 7 residues processed: 93 average time/residue: 0.2732 time to fit residues: 35.4162 Evaluate side-chains 85 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 429 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.8696 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10686 Z= 0.184 Angle : 0.556 8.438 14558 Z= 0.259 Chirality : 0.043 0.330 1692 Planarity : 0.003 0.030 1786 Dihedral : 10.037 89.645 2080 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.89 % Allowed : 16.92 % Favored : 81.19 % 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: -4.75 (0.19), residues: 1264 helix: -3.39 (0.15), residues: 706 sheet: -0.68 (0.51), residues: 102 loop : -3.03 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 477 HIS 0.002 0.001 HIS A 607 PHE 0.010 0.001 PHE A 573 TYR 0.007 0.001 TYR A 21 ARG 0.003 0.000 ARG B 66 *********************** 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 99 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 1.123 Fit side-chains REVERT: A 166 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8468 (pp) REVERT: A 543 GLU cc_start: 0.7459 (mt-10) cc_final: 0.6906 (mt-10) REVERT: B 166 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8480 (pp) REVERT: B 543 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6929 (mt-10) outliers start: 20 outliers final: 14 residues processed: 93 average time/residue: 0.2523 time to fit residues: 32.6425 Evaluate side-chains 91 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.0970 chunk 69 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 90 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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: 0.8737 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10686 Z= 0.323 Angle : 0.625 9.003 14558 Z= 0.294 Chirality : 0.046 0.327 1692 Planarity : 0.004 0.031 1786 Dihedral : 9.929 83.979 2080 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.27 % Allowed : 17.11 % Favored : 80.62 % 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: -4.71 (0.19), residues: 1264 helix: -3.36 (0.15), residues: 716 sheet: -0.75 (0.51), residues: 102 loop : -2.95 (0.24), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 477 HIS 0.002 0.001 HIS A 159 PHE 0.015 0.001 PHE B 573 TYR 0.007 0.001 TYR A 21 ARG 0.003 0.000 ARG A 66 *********************** 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 94 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 70 time to evaluate : 1.276 Fit side-chains REVERT: A 166 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8442 (pp) REVERT: A 507 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7828 (tt) REVERT: A 543 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6952 (mt-10) REVERT: B 166 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8443 (pp) REVERT: B 507 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7827 (tt) REVERT: B 543 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6908 (mt-10) outliers start: 24 outliers final: 16 residues processed: 88 average time/residue: 0.2540 time to fit residues: 31.0538 Evaluate side-chains 93 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8678 moved from start: 0.1772 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= 0.140 Angle : 0.530 8.168 14558 Z= 0.248 Chirality : 0.042 0.307 1692 Planarity : 0.003 0.029 1786 Dihedral : 9.117 87.258 2080 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.98 % Allowed : 18.15 % Favored : 79.87 % 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: -4.31 (0.20), residues: 1264 helix: -3.09 (0.16), residues: 714 sheet: -0.16 (0.55), residues: 90 loop : -2.76 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 337 HIS 0.001 0.000 HIS B 607 PHE 0.016 0.001 PHE B 16 TYR 0.007 0.001 TYR A 21 ARG 0.003 0.000 ARG A 66 *********************** 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 108 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 1.136 Fit side-chains REVERT: A 164 ASP cc_start: 0.8663 (t70) cc_final: 0.8225 (t0) REVERT: A 166 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8534 (pp) REVERT: A 507 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7610 (tt) REVERT: A 543 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6878 (mt-10) REVERT: B 164 ASP cc_start: 0.8653 (t70) cc_final: 0.8213 (t0) REVERT: B 166 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8538 (pp) REVERT: B 507 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7599 (tt) REVERT: B 543 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6892 (mt-10) outliers start: 21 outliers final: 13 residues processed: 101 average time/residue: 0.2402 time to fit residues: 34.2073 Evaluate side-chains 98 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 76 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.8700 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10686 Z= 0.215 Angle : 0.563 8.560 14558 Z= 0.263 Chirality : 0.043 0.313 1692 Planarity : 0.004 0.049 1786 Dihedral : 9.102 84.950 2080 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.80 % Allowed : 19.28 % Favored : 78.92 % 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: -4.17 (0.21), residues: 1264 helix: -2.97 (0.16), residues: 716 sheet: -0.43 (0.52), residues: 100 loop : -2.65 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 477 HIS 0.001 0.001 HIS A 135 PHE 0.013 0.001 PHE A 16 TYR 0.007 0.001 TYR A 21 ARG 0.004 0.000 ARG A 66 *********************** 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 101 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.112 Fit side-chains REVERT: A 166 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8469 (pp) REVERT: A 507 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7702 (tt) REVERT: A 543 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6876 (mt-10) REVERT: B 166 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8476 (pp) REVERT: B 507 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7703 (tt) REVERT: B 543 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6873 (mt-10) outliers start: 19 outliers final: 14 residues processed: 95 average time/residue: 0.2612 time to fit residues: 34.5701 Evaluate side-chains 95 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 572 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 0.0010 chunk 95 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- 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: 0.8677 moved from start: 0.1910 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= 0.159 Angle : 0.537 8.125 14558 Z= 0.250 Chirality : 0.042 0.306 1692 Planarity : 0.003 0.034 1786 Dihedral : 8.887 85.788 2080 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.80 % Allowed : 19.28 % Favored : 78.92 % 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: -3.97 (0.21), residues: 1264 helix: -2.84 (0.17), residues: 720 sheet: 0.11 (0.57), residues: 86 loop : -2.55 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 477 HIS 0.001 0.000 HIS A 135 PHE 0.016 0.001 PHE B 16 TYR 0.007 0.001 TYR A 21 ARG 0.004 0.000 ARG B 66 *********************** 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 96 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 1.120 Fit side-chains REVERT: A 166 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8519 (pp) REVERT: A 507 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7636 (tt) REVERT: A 543 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6859 (mt-10) REVERT: B 166 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8542 (pp) REVERT: B 507 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7651 (tt) REVERT: B 543 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6853 (mt-10) outliers start: 19 outliers final: 14 residues processed: 89 average time/residue: 0.2640 time to fit residues: 32.8827 Evaluate side-chains 95 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 572 VAL 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: 0.1980 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.0670 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 119 optimal weight: 0.0370 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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: 0.8628 moved from start: 0.2129 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 : 0.511 7.676 14558 Z= 0.238 Chirality : 0.040 0.296 1692 Planarity : 0.003 0.029 1786 Dihedral : 8.567 88.963 2080 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.23 % Allowed : 20.13 % Favored : 78.64 % 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: -3.61 (0.21), residues: 1264 helix: -2.52 (0.18), residues: 702 sheet: 0.22 (0.58), residues: 86 loop : -2.45 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 337 HIS 0.001 0.000 HIS B 607 PHE 0.012 0.001 PHE A 16 TYR 0.006 0.000 TYR A 21 ARG 0.004 0.000 ARG A 66 *********************** 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 97 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 1.335 Fit side-chains REVERT: A 164 ASP cc_start: 0.8559 (t70) cc_final: 0.8113 (t0) REVERT: A 166 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8507 (pp) REVERT: A 507 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7532 (tt) REVERT: A 543 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6813 (mt-10) REVERT: B 164 ASP cc_start: 0.8566 (t70) cc_final: 0.8121 (t0) REVERT: B 507 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7532 (tt) REVERT: B 543 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6765 (mt-10) REVERT: B 544 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7979 (tp30) outliers start: 13 outliers final: 3 residues processed: 93 average time/residue: 0.2785 time to fit residues: 35.3214 Evaluate side-chains 86 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 507 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.8643 moved from start: 0.2142 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= 0.140 Angle : 0.524 8.087 14558 Z= 0.241 Chirality : 0.041 0.300 1692 Planarity : 0.003 0.031 1786 Dihedral : 8.568 88.192 2080 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.66 % Allowed : 20.32 % Favored : 79.02 % 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: -3.51 (0.21), residues: 1264 helix: -2.42 (0.18), residues: 720 sheet: -0.44 (0.67), residues: 60 loop : -2.19 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 337 HIS 0.001 0.000 HIS B 607 PHE 0.012 0.001 PHE B 16 TYR 0.006 0.001 TYR A 21 ARG 0.004 0.000 ARG A 66 ********************** 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 89 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 1.113 Fit side-chains REVERT: A 164 ASP cc_start: 0.8575 (t70) cc_final: 0.8116 (t0) REVERT: A 166 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8532 (pp) REVERT: A 507 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7613 (tt) REVERT: A 543 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6802 (mt-10) REVERT: B 164 ASP cc_start: 0.8509 (t70) cc_final: 0.8076 (t0) REVERT: B 486 ARG cc_start: 0.8162 (ttp80) cc_final: 0.7956 (ttp80) REVERT: B 507 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7610 (tt) REVERT: B 543 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6748 (mt-10) REVERT: B 544 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7985 (tp30) outliers start: 7 outliers final: 4 residues processed: 87 average time/residue: 0.2860 time to fit residues: 33.6436 Evaluate side-chains 86 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 507 LEU 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: 2.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 0.0000 chunk 5 optimal weight: 2.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.115731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.087458 restraints weight = 14850.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.090584 restraints weight = 8609.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.092608 restraints weight = 6008.876| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2212 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= 0.131 Angle : 0.520 7.746 14558 Z= 0.240 Chirality : 0.041 0.298 1692 Planarity : 0.003 0.030 1786 Dihedral : 8.439 88.721 2080 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.85 % Allowed : 20.42 % Favored : 78.73 % 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: -3.36 (0.21), residues: 1264 helix: -2.27 (0.18), residues: 720 sheet: 0.22 (0.59), residues: 80 loop : -2.37 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 337 HIS 0.001 0.000 HIS B 607 PHE 0.008 0.001 PHE B 573 TYR 0.006 0.000 TYR A 21 ARG 0.006 0.000 ARG A 486 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1924.77 seconds wall clock time: 35 minutes 25.91 seconds (2125.91 seconds total)