Starting phenix.real_space_refine (version: dev) on Thu Feb 23 14:04:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt2_26108/02_2023/7tt2_26108.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt2_26108/02_2023/7tt2_26108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt2_26108/02_2023/7tt2_26108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt2_26108/02_2023/7tt2_26108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt2_26108/02_2023/7tt2_26108.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tt2_26108/02_2023/7tt2_26108.pdb" } resolution = 4.2 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= 0.006 sd= 0.065 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 Process input model Symmetric amino acids flipped Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 688": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 1296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 1298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 20355 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3390 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "C" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 675 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1381 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "B" Number of atoms: 5199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 5199 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 11, 'TRANS': 338} Chain breaks: 2 Chain: "A" Number of atoms: 9425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 9425 Classifications: {'peptide': 610} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 585} Chain breaks: 4 Chain: "P" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 285 Classifications: {'peptide': 18} Modifications used: {'COO': 1} Link IDs: {'TRANS': 17} Chain breaks: 1 Time building chain proxies: 9.73, per 1000 atoms: 0.48 Number of scatterers: 20355 At special positions: 0 Unit cell: (106.308, 127.785, 137.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 2031 8.00 N 1768 7.00 C 6551 6.00 H 9973 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS P1299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 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: 15.67 Conformation dependent library (CDL) restraints added in 1.8 seconds 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2420 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 24.2% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 47 through 60 removed outlier: 3.558A pdb=" N LEU D 58 " --> pdb=" O GLN D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 removed outlier: 3.668A pdb=" N ALA D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.790A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.659A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.444A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.828A pdb=" N TYR D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.944A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.523A pdb=" N MET D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.569A pdb=" N ASN D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 43 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'E' and resid 23 through 27 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.669A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 232 removed outlier: 3.529A pdb=" N GLY A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.525A pdb=" N ILE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 313 Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.643A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 4.187A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 730 Processing sheet with id=AA1, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.790A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.779A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.891A pdb=" N GLY B 385 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 68 removed outlier: 5.569A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 111 through 117 removed outlier: 6.241A pdb=" N GLY B 114 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY B 125 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.734A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.848A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.823A pdb=" N LEU B 267 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.650A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.781A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 179 through 183 removed outlier: 4.150A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR A 255 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL A 245 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR A 257 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR A 243 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASN A 259 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.308A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 13.155A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 10.536A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 12.157A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.162A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.805A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.360A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 11.645A pdb=" N GLU A 420 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N GLN A 411 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ARG A 404 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 802 through 806 removed outlier: 6.367A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 710 " --> pdb=" O TRP A 745 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 445 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS A 425 " --> pdb=" O GLN A 445 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.263A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1263 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: 7.45 Time building geometry restraints manager: 16.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9973 1.03 - 1.23: 202 1.23 - 1.43: 4422 1.43 - 1.63: 5926 1.63 - 1.82: 60 Bond restraints: 20583 Sorted by residual: bond pdb=" C VAL A 444 " pdb=" N GLN A 445 " ideal model delta sigma weight residual 1.333 1.316 0.017 1.30e-02 5.92e+03 1.80e+00 bond pdb=" N ARG B 195 " pdb=" CA ARG B 195 " ideal model delta sigma weight residual 1.456 1.443 0.013 1.22e-02 6.72e+03 1.17e+00 bond pdb=" CB TRP A 376 " pdb=" CG TRP A 376 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.09e+00 bond pdb=" CA GLY B 169 " pdb=" C GLY B 169 " ideal model delta sigma weight residual 1.510 1.496 0.015 1.41e-02 5.03e+03 1.07e+00 bond pdb=" CG ARG A 366 " pdb=" CD ARG A 366 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.06e+00 ... (remaining 20578 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.39: 323 106.39 - 113.32: 23435 113.32 - 120.26: 7079 120.26 - 127.20: 6021 127.20 - 134.13: 123 Bond angle restraints: 36981 Sorted by residual: angle pdb=" N GLY B 214 " pdb=" CA GLY B 214 " pdb=" C GLY B 214 " ideal model delta sigma weight residual 115.32 108.79 6.53 1.48e+00 4.57e-01 1.95e+01 angle pdb=" N GLY A 424 " pdb=" CA GLY A 424 " pdb=" C GLY A 424 " ideal model delta sigma weight residual 113.18 104.17 9.01 2.37e+00 1.78e-01 1.44e+01 angle pdb=" C THR B 166 " pdb=" N SER B 167 " pdb=" CA SER B 167 " ideal model delta sigma weight residual 120.99 127.88 -6.89 1.86e+00 2.89e-01 1.37e+01 angle pdb=" N LEU B 192 " pdb=" CA LEU B 192 " pdb=" C LEU B 192 " ideal model delta sigma weight residual 110.80 118.52 -7.72 2.13e+00 2.20e-01 1.31e+01 angle pdb=" N GLY B 169 " pdb=" CA GLY B 169 " pdb=" C GLY B 169 " ideal model delta sigma weight residual 114.76 108.78 5.98 1.70e+00 3.46e-01 1.24e+01 ... (remaining 36976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 7995 17.34 - 34.69: 190 34.69 - 52.03: 70 52.03 - 69.38: 33 69.38 - 86.72: 10 Dihedral angle restraints: 8298 sinusoidal: 3761 harmonic: 4537 Sorted by residual: dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -140.48 54.48 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CA PRO B 330 " pdb=" C PRO B 330 " pdb=" N VAL B 331 " pdb=" CA VAL B 331 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASP B 138 " pdb=" C ASP B 138 " pdb=" N GLY B 139 " pdb=" CA GLY B 139 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 8295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1044 0.042 - 0.084: 369 0.084 - 0.125: 120 0.125 - 0.167: 27 0.167 - 0.209: 3 Chirality restraints: 1563 Sorted by residual: chirality pdb=" CA ARG D 166 " pdb=" N ARG D 166 " pdb=" C ARG D 166 " pdb=" CB ARG D 166 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ARG D 61 " pdb=" N ARG D 61 " pdb=" C ARG D 61 " pdb=" CB ARG D 61 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.26e-01 chirality pdb=" CA HIS E 83 " pdb=" N HIS E 83 " pdb=" C HIS E 83 " pdb=" CB HIS E 83 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.19e-01 ... (remaining 1560 not shown) Planarity restraints: 3155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 34 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C GLU D 34 " 0.061 2.00e-02 2.50e+03 pdb=" O GLU D 34 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE D 35 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 166 " -0.016 2.00e-02 2.50e+03 3.38e-02 1.15e+01 pdb=" C THR B 166 " 0.058 2.00e-02 2.50e+03 pdb=" O THR B 166 " -0.023 2.00e-02 2.50e+03 pdb=" N SER B 167 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 86 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.13e+01 pdb=" C PRO D 86 " 0.058 2.00e-02 2.50e+03 pdb=" O PRO D 86 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU D 87 " -0.020 2.00e-02 2.50e+03 ... (remaining 3152 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 315 2.05 - 2.69: 30640 2.69 - 3.32: 55542 3.32 - 3.96: 72188 3.96 - 4.60: 111616 Nonbonded interactions: 270301 Sorted by model distance: nonbonded pdb=" O VAL E 27 " pdb=" HE2 HIS E 83 " model vdw 1.409 1.850 nonbonded pdb=" HD1 HIS A 533 " pdb=" OD1 ASP A 568 " model vdw 1.462 1.850 nonbonded pdb=" O TYR B 263 " pdb="HE22 GLN B 301 " model vdw 1.563 1.850 nonbonded pdb=" HH TYR E 28 " pdb=" OE2 GLU A 521 " model vdw 1.571 1.850 nonbonded pdb=" HH TYR A 674 " pdb=" OD2 ASP A 704 " model vdw 1.571 1.850 ... (remaining 270296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 6551 2.51 5 N 1768 2.21 5 O 2031 1.98 5 H 9973 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.920 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: 0.320 Extract box with map and model: 4.900 Check model and map are aligned: 0.290 Process input model: 62.500 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.190 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 10610 Z= 0.270 Angle : 0.913 9.008 14415 Z= 0.559 Chirality : 0.048 0.209 1563 Planarity : 0.005 0.073 1896 Dihedral : 10.679 86.722 3819 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1302 helix: 0.43 (0.28), residues: 264 sheet: 0.89 (0.24), residues: 404 loop : 0.51 (0.24), residues: 634 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 0.5177 time to fit residues: 303.1827 Evaluate side-chains 251 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.627 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 359 GLN A 280 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 10610 Z= 0.177 Angle : 0.576 4.744 14415 Z= 0.324 Chirality : 0.043 0.169 1563 Planarity : 0.004 0.051 1896 Dihedral : 4.948 50.090 1453 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.22), residues: 1302 helix: 1.71 (0.30), residues: 267 sheet: 0.82 (0.24), residues: 413 loop : 0.64 (0.24), residues: 622 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.4968 time to fit residues: 210.2680 Evaluate side-chains 234 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.671 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 0.0870 chunk 105 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 94 optimal weight: 0.1980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS B 359 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 10610 Z= 0.142 Angle : 0.518 5.135 14415 Z= 0.286 Chirality : 0.042 0.155 1563 Planarity : 0.003 0.043 1896 Dihedral : 4.707 41.373 1453 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.22), residues: 1302 helix: 2.00 (0.30), residues: 266 sheet: 0.72 (0.24), residues: 408 loop : 0.44 (0.24), residues: 628 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.4834 time to fit residues: 201.2854 Evaluate side-chains 241 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 1.675 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 10610 Z= 0.283 Angle : 0.556 4.551 14415 Z= 0.311 Chirality : 0.042 0.154 1563 Planarity : 0.004 0.047 1896 Dihedral : 4.725 22.148 1453 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1302 helix: 1.71 (0.30), residues: 265 sheet: 0.41 (0.24), residues: 416 loop : 0.08 (0.24), residues: 621 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.5149 time to fit residues: 199.2315 Evaluate side-chains 224 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.748 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 112 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 10610 Z= 0.236 Angle : 0.532 4.433 14415 Z= 0.295 Chirality : 0.042 0.163 1563 Planarity : 0.004 0.038 1896 Dihedral : 4.680 25.946 1453 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.23), residues: 1302 helix: 1.61 (0.30), residues: 270 sheet: 0.30 (0.24), residues: 413 loop : -0.10 (0.25), residues: 619 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.5145 time to fit residues: 192.7360 Evaluate side-chains 229 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.649 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 280 HIS ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.068 10610 Z= 0.389 Angle : 0.616 6.080 14415 Z= 0.348 Chirality : 0.043 0.160 1563 Planarity : 0.005 0.047 1896 Dihedral : 5.026 29.121 1453 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % 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: -0.16 (0.22), residues: 1302 helix: 0.82 (0.29), residues: 272 sheet: 0.10 (0.24), residues: 416 loop : -0.59 (0.25), residues: 614 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 262 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 263 average time/residue: 0.5170 time to fit residues: 188.3488 Evaluate side-chains 216 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.771 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 10610 Z= 0.200 Angle : 0.527 4.461 14415 Z= 0.290 Chirality : 0.042 0.150 1563 Planarity : 0.003 0.035 1896 Dihedral : 4.816 36.486 1453 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: 0.07 (0.23), residues: 1302 helix: 1.28 (0.30), residues: 272 sheet: 0.05 (0.24), residues: 406 loop : -0.42 (0.25), residues: 624 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.5070 time to fit residues: 187.2957 Evaluate side-chains 223 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 7.9990 chunk 74 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 10610 Z= 0.153 Angle : 0.511 7.213 14415 Z= 0.277 Chirality : 0.042 0.154 1563 Planarity : 0.003 0.039 1896 Dihedral : 4.664 38.098 1453 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1302 helix: 1.52 (0.30), residues: 270 sheet: 0.15 (0.24), residues: 410 loop : -0.41 (0.25), residues: 622 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.4980 time to fit residues: 185.6892 Evaluate side-chains 228 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.640 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 123 optimal weight: 0.2980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.6034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 10610 Z= 0.314 Angle : 0.561 4.990 14415 Z= 0.312 Chirality : 0.042 0.148 1563 Planarity : 0.004 0.043 1896 Dihedral : 4.850 38.024 1453 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.23), residues: 1302 helix: 1.05 (0.30), residues: 274 sheet: 0.01 (0.24), residues: 412 loop : -0.59 (0.25), residues: 616 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.5069 time to fit residues: 184.9970 Evaluate side-chains 216 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.718 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 129 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 10610 Z= 0.182 Angle : 0.514 4.878 14415 Z= 0.281 Chirality : 0.042 0.149 1563 Planarity : 0.003 0.037 1896 Dihedral : 4.738 41.878 1453 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.23), residues: 1302 helix: 1.29 (0.30), residues: 271 sheet: 0.11 (0.24), residues: 404 loop : -0.58 (0.25), residues: 627 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.5219 time to fit residues: 186.6956 Evaluate side-chains 221 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.688 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 0.0970 chunk 43 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.0570 chunk 90 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN ** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.166827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.127819 restraints weight = 57052.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.132550 restraints weight = 39796.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.133085 restraints weight = 29958.458| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 10610 Z= 0.134 Angle : 0.499 4.967 14415 Z= 0.268 Chirality : 0.042 0.158 1563 Planarity : 0.003 0.033 1896 Dihedral : 4.543 43.006 1453 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.23), residues: 1302 helix: 1.63 (0.30), residues: 270 sheet: 0.23 (0.25), residues: 403 loop : -0.51 (0.25), residues: 629 =============================================================================== Job complete usr+sys time: 4968.12 seconds wall clock time: 88 minutes 4.78 seconds (5284.78 seconds total)