Starting phenix.real_space_refine on Sat Apr 6 18:58:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjo_33876/04_2024/7yjo_33876_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjo_33876/04_2024/7yjo_33876.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjo_33876/04_2024/7yjo_33876_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjo_33876/04_2024/7yjo_33876_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjo_33876/04_2024/7yjo_33876_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjo_33876/04_2024/7yjo_33876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjo_33876/04_2024/7yjo_33876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjo_33876/04_2024/7yjo_33876_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yjo_33876/04_2024/7yjo_33876_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 22 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 49 5.16 5 C 5651 2.51 5 N 1482 2.21 5 O 1586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ARG 162": "NH1" <-> "NH2" Residue "A ASP 171": "OD1" <-> "OD2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A ASP 424": "OD1" <-> "OD2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 443": "OD1" <-> "OD2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "B TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 117": "OD1" <-> "OD2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B GLU 255": "OE1" <-> "OE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ARG 441": "NH1" <-> "NH2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B ASP 452": "OD1" <-> "OD2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "C ARG 6": "NH1" <-> "NH2" Residue "C ARG 25": "NH1" <-> "NH2" Residue "C PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 45": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8769 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3226 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 400} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3643 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 20, 'TRANS': 446} Chain breaks: 1 Chain: "D" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1201 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "E" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 195 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 24} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 436 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'Z1T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.05, per 1000 atoms: 0.58 Number of scatterers: 8769 At special positions: 0 Unit cell: (88.56, 82.08, 118.8, 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 49 16.00 P 1 15.00 O 1586 8.00 N 1482 7.00 C 5651 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: 3.24 Conformation dependent library (CDL) restraints added in 1.8 seconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 6 sheets defined 42.7% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 66 through 75 removed outlier: 3.673A pdb=" N ASP A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 139 removed outlier: 3.732A pdb=" N SER A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.545A pdb=" N THR A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 183 No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 186 through 189 No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 225 through 238 Processing helix chain 'A' and resid 264 through 274 removed outlier: 3.704A pdb=" N LYS A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 350 through 365 removed outlier: 3.527A pdb=" N ALA A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 384 removed outlier: 3.769A pdb=" N LYS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 3.514A pdb=" N LEU A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 469 No H-bonds generated for 'chain 'A' and resid 466 through 469' Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.677A pdb=" N PHE B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE B 32 " --> pdb=" O PHE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 120 through 131 removed outlier: 3.513A pdb=" N GLU B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 159 removed outlier: 3.592A pdb=" N GLU B 152 " --> pdb=" O HIS B 148 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 removed outlier: 3.893A pdb=" N ASN B 174 " --> pdb=" O GLY B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 181 No H-bonds generated for 'chain 'B' and resid 178 through 181' Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 217 through 228 removed outlier: 3.567A pdb=" N GLU B 221 " --> pdb=" O PRO B 217 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 269 Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 324 through 333 removed outlier: 3.618A pdb=" N HIS B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 Processing helix chain 'B' and resid 345 through 359 removed outlier: 3.637A pdb=" N GLN B 350 " --> pdb=" O PRO B 346 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 removed outlier: 3.689A pdb=" N LEU B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN B 379 " --> pdb=" O ARG B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 421 removed outlier: 3.599A pdb=" N ILE B 411 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Proline residue: B 412 - end of helix removed outlier: 3.532A pdb=" N ARG B 416 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 419 " --> pdb=" O ARG B 416 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG B 420 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 467 removed outlier: 4.101A pdb=" N ARG B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 22 removed outlier: 3.725A pdb=" N MET D 22 " --> pdb=" O GLU D 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 19 through 22' Processing helix chain 'D' and resid 26 through 44 removed outlier: 3.529A pdb=" N LEU D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 69 removed outlier: 3.587A pdb=" N VAL D 55 " --> pdb=" O MET D 51 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE D 61 " --> pdb=" O ASN D 57 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 64 " --> pdb=" O HIS D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 95 removed outlier: 6.062A pdb=" N ASP D 93 " --> pdb=" O TRP D 89 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ASN D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY D 95 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 118 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 124 through 141 removed outlier: 3.512A pdb=" N PHE D 128 " --> pdb=" O HIS D 124 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU D 129 " --> pdb=" O PRO D 125 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 134 " --> pdb=" O ASN D 130 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 53 removed outlier: 4.070A pdb=" N THR E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 removed outlier: 3.515A pdb=" N TYR C 9 " --> pdb=" O GLN C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 19 No H-bonds generated for 'chain 'C' and resid 17 through 19' Processing helix chain 'C' and resid 22 through 41 removed outlier: 3.556A pdb=" N PHE C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU C 31 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.522A pdb=" N THR A 104 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 171 through 175 removed outlier: 3.692A pdb=" N ASP A 171 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 327 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 281 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 195 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL A 250 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 197 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N GLU A 252 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR A 216 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ALA A 198 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 218 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 390 through 392 Processing sheet with id= D, first strand: chain 'B' and resid 78 through 81 Processing sheet with id= E, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.744A pdb=" N LEU B 187 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VAL B 245 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE B 189 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N GLU B 247 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ASP B 191 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR B 208 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N SER B 190 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG B 210 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 426 through 428 removed outlier: 3.921A pdb=" N VAL B 426 " --> pdb=" O ARG B 441 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 864 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: 2.31 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1670 1.32 - 1.45: 2208 1.45 - 1.57: 5017 1.57 - 1.69: 1 1.69 - 1.81: 76 Bond restraints: 8972 Sorted by residual: bond pdb=" C14 Z1T D 201 " pdb=" C15 Z1T D 201 " ideal model delta sigma weight residual 1.343 1.523 -0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" C HIS B 236 " pdb=" N ARG B 237 " ideal model delta sigma weight residual 1.330 1.201 0.129 1.47e-02 4.63e+03 7.75e+01 bond pdb=" C19 Z1T D 201 " pdb=" N1 Z1T D 201 " ideal model delta sigma weight residual 1.481 1.331 0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" C4 PLS B 601 " pdb=" C5 PLS B 601 " ideal model delta sigma weight residual 1.355 1.483 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C3 PLS B 601 " pdb=" C4 PLS B 601 " ideal model delta sigma weight residual 1.355 1.479 -0.124 2.00e-02 2.50e+03 3.87e+01 ... (remaining 8967 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.97: 185 105.97 - 113.14: 4831 113.14 - 120.32: 3662 120.32 - 127.49: 3366 127.49 - 134.66: 97 Bond angle restraints: 12141 Sorted by residual: angle pdb=" C14 Z1T D 201 " pdb=" C15 Z1T D 201 " pdb=" C16 Z1T D 201 " ideal model delta sigma weight residual 152.64 115.08 37.56 3.00e+00 1.11e-01 1.57e+02 angle pdb=" N PHE B 430 " pdb=" CA PHE B 430 " pdb=" C PHE B 430 " ideal model delta sigma weight residual 109.81 123.69 -13.88 2.21e+00 2.05e-01 3.95e+01 angle pdb=" N HIS D 124 " pdb=" CA HIS D 124 " pdb=" C HIS D 124 " ideal model delta sigma weight residual 109.81 120.75 -10.94 2.21e+00 2.05e-01 2.45e+01 angle pdb=" C HIS D 124 " pdb=" N PRO D 125 " pdb=" CA PRO D 125 " ideal model delta sigma weight residual 119.32 114.33 4.99 1.14e+00 7.69e-01 1.92e+01 angle pdb=" N TYR B 85 " pdb=" CA TYR B 85 " pdb=" C TYR B 85 " ideal model delta sigma weight residual 111.71 117.32 -5.61 1.34e+00 5.57e-01 1.75e+01 ... (remaining 12136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4841 17.98 - 35.96: 400 35.96 - 53.94: 72 53.94 - 71.92: 14 71.92 - 89.91: 10 Dihedral angle restraints: 5337 sinusoidal: 2142 harmonic: 3195 Sorted by residual: dihedral pdb=" CA ASP D 79 " pdb=" C ASP D 79 " pdb=" N GLN D 80 " pdb=" CA GLN D 80 " ideal model delta harmonic sigma weight residual 180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" N PHE B 430 " pdb=" C PHE B 430 " pdb=" CA PHE B 430 " pdb=" CB PHE B 430 " ideal model delta harmonic sigma weight residual 122.80 135.22 -12.42 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" CA VAL A 288 " pdb=" C VAL A 288 " pdb=" N LEU A 289 " pdb=" CA LEU A 289 " ideal model delta harmonic sigma weight residual -180.00 -155.64 -24.36 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 5334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1286 0.117 - 0.233: 65 0.233 - 0.350: 1 0.350 - 0.466: 1 0.466 - 0.583: 1 Chirality restraints: 1354 Sorted by residual: chirality pdb=" CA PHE B 430 " pdb=" N PHE B 430 " pdb=" C PHE B 430 " pdb=" CB PHE B 430 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.50e+00 chirality pdb=" CA HIS D 124 " pdb=" N HIS D 124 " pdb=" C HIS D 124 " pdb=" CB HIS D 124 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CA PHE B 79 " pdb=" N PHE B 79 " pdb=" C PHE B 79 " pdb=" CB PHE B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1351 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 380 " -0.017 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C LEU A 380 " 0.062 2.00e-02 2.50e+03 pdb=" O LEU A 380 " -0.023 2.00e-02 2.50e+03 pdb=" N TRP A 381 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 20 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C TRP D 20 " 0.041 2.00e-02 2.50e+03 pdb=" O TRP D 20 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE D 21 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 406 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" C TYR B 406 " 0.036 2.00e-02 2.50e+03 pdb=" O TYR B 406 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN B 407 " -0.012 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 336 2.71 - 3.26: 8277 3.26 - 3.80: 13068 3.80 - 4.35: 17354 4.35 - 4.90: 30001 Nonbonded interactions: 69036 Sorted by model distance: nonbonded pdb=" O SER B 132 " pdb=" OG SER B 132 " model vdw 2.161 2.440 nonbonded pdb=" O PHE B 430 " pdb=" O THR B 433 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR B 287 " pdb=" OE2 GLU B 293 " model vdw 2.262 2.440 nonbonded pdb=" OE2 GLU A 66 " pdb=" NH2 ARG B 225 " model vdw 2.297 2.520 nonbonded pdb=" NH1 ARG B 373 " pdb=" O ALA B 446 " model vdw 2.310 2.520 ... (remaining 69031 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 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 4.090 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.980 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 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 : 0.011 0.180 8972 Z= 0.716 Angle : 1.045 37.559 12141 Z= 0.585 Chirality : 0.063 0.583 1354 Planarity : 0.006 0.045 1522 Dihedral : 14.208 89.905 3289 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 0.74 % Allowed : 0.84 % Favored : 98.42 % Cbeta Deviations : 0.10 % 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: -1.89 (0.24), residues: 1094 helix: -1.18 (0.21), residues: 526 sheet: -0.60 (0.46), residues: 121 loop : -1.34 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 239 HIS 0.007 0.002 HIS A 299 PHE 0.025 0.003 PHE A 220 TYR 0.024 0.003 TYR A 177 ARG 0.009 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.031 Fit side-chains REVERT: B 31 ARG cc_start: 0.7749 (ttp-170) cc_final: 0.7019 (ttt90) REVERT: B 475 GLU cc_start: 0.5859 (OUTLIER) cc_final: 0.5659 (pp20) REVERT: C 2 ASN cc_start: 0.7983 (p0) cc_final: 0.7778 (p0) outliers start: 7 outliers final: 2 residues processed: 110 average time/residue: 1.6034 time to fit residues: 185.7350 Evaluate side-chains 91 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 475 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 97 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN B 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8972 Z= 0.168 Angle : 0.553 7.756 12141 Z= 0.287 Chirality : 0.044 0.154 1354 Planarity : 0.004 0.051 1522 Dihedral : 8.315 81.708 1257 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.06 % Allowed : 6.97 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.26), residues: 1094 helix: -0.18 (0.23), residues: 530 sheet: 0.19 (0.50), residues: 116 loop : -1.01 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 204 HIS 0.003 0.001 HIS D 124 PHE 0.022 0.001 PHE A 183 TYR 0.011 0.001 TYR A 255 ARG 0.006 0.000 ARG E 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 1.080 Fit side-chains REVERT: B 30 ARG cc_start: 0.7451 (tpt170) cc_final: 0.5684 (tpp-160) REVERT: B 31 ARG cc_start: 0.7576 (ttp-170) cc_final: 0.6997 (ttt90) REVERT: C 2 ASN cc_start: 0.7700 (p0) cc_final: 0.7459 (p0) outliers start: 10 outliers final: 4 residues processed: 109 average time/residue: 1.5021 time to fit residues: 173.3161 Evaluate side-chains 102 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain D residue 22 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8972 Z= 0.203 Angle : 0.541 7.800 12141 Z= 0.279 Chirality : 0.044 0.160 1354 Planarity : 0.004 0.049 1522 Dihedral : 7.671 79.818 1251 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.27 % Allowed : 9.19 % Favored : 89.55 % 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: -0.47 (0.26), residues: 1094 helix: 0.19 (0.24), residues: 529 sheet: 0.20 (0.51), residues: 111 loop : -0.93 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 204 HIS 0.003 0.001 HIS A 299 PHE 0.024 0.002 PHE A 183 TYR 0.011 0.001 TYR B 274 ARG 0.003 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.061 Fit side-chains REVERT: A 107 ASN cc_start: 0.8695 (t0) cc_final: 0.8488 (t0) REVERT: B 31 ARG cc_start: 0.7632 (ttp-170) cc_final: 0.7081 (ttt90) REVERT: B 475 GLU cc_start: 0.5834 (OUTLIER) cc_final: 0.5600 (pp20) outliers start: 12 outliers final: 4 residues processed: 110 average time/residue: 1.4207 time to fit residues: 166.0723 Evaluate side-chains 97 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 475 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN D 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8972 Z= 0.188 Angle : 0.518 7.420 12141 Z= 0.269 Chirality : 0.044 0.154 1354 Planarity : 0.004 0.050 1522 Dihedral : 7.569 78.769 1251 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.37 % Allowed : 10.67 % Favored : 87.96 % 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: -0.26 (0.26), residues: 1094 helix: 0.33 (0.24), residues: 531 sheet: 0.32 (0.51), residues: 111 loop : -0.80 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 204 HIS 0.003 0.001 HIS B 279 PHE 0.023 0.001 PHE A 183 TYR 0.011 0.001 TYR B 274 ARG 0.005 0.000 ARG E 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 1.093 Fit side-chains REVERT: A 107 ASN cc_start: 0.8675 (t0) cc_final: 0.8461 (t0) REVERT: B 31 ARG cc_start: 0.7602 (ttp-170) cc_final: 0.7070 (ttt90) REVERT: B 475 GLU cc_start: 0.5830 (OUTLIER) cc_final: 0.5585 (pp20) outliers start: 13 outliers final: 7 residues processed: 105 average time/residue: 1.4583 time to fit residues: 162.2715 Evaluate side-chains 103 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 475 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8972 Z= 0.249 Angle : 0.553 8.052 12141 Z= 0.286 Chirality : 0.045 0.161 1354 Planarity : 0.004 0.050 1522 Dihedral : 7.696 78.514 1251 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.69 % Allowed : 10.77 % Favored : 87.54 % 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: -0.27 (0.26), residues: 1094 helix: 0.32 (0.24), residues: 532 sheet: 0.37 (0.51), residues: 111 loop : -0.81 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 204 HIS 0.004 0.001 HIS A 299 PHE 0.026 0.002 PHE A 183 TYR 0.013 0.001 TYR B 274 ARG 0.005 0.000 ARG E 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 0.967 Fit side-chains REVERT: A 107 ASN cc_start: 0.8693 (t0) cc_final: 0.8479 (t0) REVERT: B 31 ARG cc_start: 0.7692 (ttp-170) cc_final: 0.7132 (ttt90) REVERT: B 475 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5646 (pp20) REVERT: C 2 ASN cc_start: 0.7749 (p0) cc_final: 0.7422 (p0) outliers start: 16 outliers final: 9 residues processed: 111 average time/residue: 1.3787 time to fit residues: 162.8608 Evaluate side-chains 106 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 475 GLU Chi-restraints excluded: chain D residue 145 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN D 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8972 Z= 0.237 Angle : 0.541 8.074 12141 Z= 0.281 Chirality : 0.045 0.160 1354 Planarity : 0.004 0.051 1522 Dihedral : 7.689 79.057 1251 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.80 % Allowed : 12.04 % Favored : 86.17 % 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 (0.26), residues: 1094 helix: 0.36 (0.24), residues: 532 sheet: 0.41 (0.51), residues: 111 loop : -0.79 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 204 HIS 0.003 0.001 HIS A 299 PHE 0.025 0.002 PHE A 183 TYR 0.012 0.001 TYR B 274 ARG 0.006 0.000 ARG E 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 1.091 Fit side-chains REVERT: A 107 ASN cc_start: 0.8688 (t0) cc_final: 0.8471 (t0) REVERT: A 366 ASN cc_start: 0.8604 (m-40) cc_final: 0.8381 (m-40) REVERT: B 31 ARG cc_start: 0.7783 (ttp-170) cc_final: 0.7264 (ttp80) REVERT: B 420 ARG cc_start: 0.8342 (ttp80) cc_final: 0.8124 (mtp85) REVERT: B 475 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5651 (pp20) outliers start: 17 outliers final: 10 residues processed: 106 average time/residue: 1.3996 time to fit residues: 157.8991 Evaluate side-chains 106 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 475 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN D 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8972 Z= 0.155 Angle : 0.488 8.288 12141 Z= 0.253 Chirality : 0.043 0.150 1354 Planarity : 0.004 0.048 1522 Dihedral : 7.378 78.549 1251 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.80 % Allowed : 12.57 % Favored : 85.64 % 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: -0.02 (0.27), residues: 1094 helix: 0.59 (0.24), residues: 529 sheet: 0.49 (0.51), residues: 111 loop : -0.77 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 204 HIS 0.002 0.000 HIS A 299 PHE 0.021 0.001 PHE A 183 TYR 0.009 0.001 TYR B 269 ARG 0.007 0.000 ARG E 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 1.013 Fit side-chains REVERT: A 107 ASN cc_start: 0.8661 (t0) cc_final: 0.8437 (t0) REVERT: A 366 ASN cc_start: 0.8541 (m-40) cc_final: 0.8249 (m-40) REVERT: B 31 ARG cc_start: 0.7650 (ttp-170) cc_final: 0.7174 (ttp80) REVERT: B 420 ARG cc_start: 0.8321 (ttp80) cc_final: 0.8116 (mtp85) REVERT: B 475 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.5723 (pp20) outliers start: 17 outliers final: 8 residues processed: 113 average time/residue: 1.5386 time to fit residues: 184.0762 Evaluate side-chains 101 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 475 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 194 ASN D 57 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8972 Z= 0.155 Angle : 0.486 8.811 12141 Z= 0.252 Chirality : 0.042 0.148 1354 Planarity : 0.004 0.046 1522 Dihedral : 7.137 78.356 1251 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.27 % Allowed : 13.73 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.18 (0.27), residues: 1094 helix: 0.77 (0.24), residues: 528 sheet: 0.56 (0.51), residues: 111 loop : -0.68 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 204 HIS 0.003 0.000 HIS A 125 PHE 0.020 0.001 PHE A 183 TYR 0.009 0.001 TYR B 274 ARG 0.006 0.000 ARG E 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.052 Fit side-chains REVERT: A 107 ASN cc_start: 0.8621 (t0) cc_final: 0.8390 (t0) REVERT: A 256 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7927 (tp-100) REVERT: A 366 ASN cc_start: 0.8443 (m-40) cc_final: 0.8187 (m-40) REVERT: B 31 ARG cc_start: 0.7653 (ttp-170) cc_final: 0.7179 (ttp80) REVERT: B 475 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.5698 (pp20) outliers start: 12 outliers final: 5 residues processed: 106 average time/residue: 1.4781 time to fit residues: 166.1364 Evaluate side-chains 102 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 475 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8972 Z= 0.261 Angle : 0.555 9.310 12141 Z= 0.287 Chirality : 0.045 0.160 1354 Planarity : 0.004 0.047 1522 Dihedral : 7.421 79.621 1251 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.48 % Allowed : 13.52 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.06 (0.26), residues: 1094 helix: 0.63 (0.24), residues: 531 sheet: 0.32 (0.50), residues: 119 loop : -0.66 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 204 HIS 0.004 0.001 HIS A 299 PHE 0.026 0.002 PHE A 183 TYR 0.013 0.001 TYR B 274 ARG 0.006 0.000 ARG E 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.975 Fit side-chains REVERT: A 107 ASN cc_start: 0.8665 (t0) cc_final: 0.8440 (t0) REVERT: A 256 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7990 (tp-100) REVERT: A 366 ASN cc_start: 0.8559 (m-40) cc_final: 0.8316 (m-40) REVERT: B 31 ARG cc_start: 0.7690 (ttp-170) cc_final: 0.7189 (ttp80) REVERT: B 475 GLU cc_start: 0.5946 (OUTLIER) cc_final: 0.5699 (pp20) outliers start: 14 outliers final: 10 residues processed: 105 average time/residue: 1.4038 time to fit residues: 156.4737 Evaluate side-chains 104 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 475 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN D 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8972 Z= 0.158 Angle : 0.494 9.051 12141 Z= 0.256 Chirality : 0.043 0.147 1354 Planarity : 0.004 0.048 1522 Dihedral : 7.225 79.147 1251 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.16 % Allowed : 14.26 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.27), residues: 1094 helix: 0.84 (0.24), residues: 530 sheet: 0.57 (0.51), residues: 111 loop : -0.66 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 204 HIS 0.002 0.000 HIS A 299 PHE 0.021 0.001 PHE A 183 TYR 0.010 0.001 TYR A 255 ARG 0.006 0.000 ARG E 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.112 Fit side-chains REVERT: A 107 ASN cc_start: 0.8614 (t0) cc_final: 0.8380 (t0) REVERT: A 366 ASN cc_start: 0.8487 (m-40) cc_final: 0.8215 (m-40) REVERT: B 31 ARG cc_start: 0.7623 (ttp-170) cc_final: 0.7129 (ttp80) REVERT: B 375 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7854 (ttt-90) REVERT: B 475 GLU cc_start: 0.5926 (OUTLIER) cc_final: 0.5698 (pp20) outliers start: 11 outliers final: 9 residues processed: 101 average time/residue: 1.4675 time to fit residues: 157.5086 Evaluate side-chains 102 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 475 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 0.0050 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 ASN D 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.113582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.090263 restraints weight = 11444.254| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.84 r_work: 0.2802 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8972 Z= 0.144 Angle : 0.480 9.163 12141 Z= 0.248 Chirality : 0.042 0.144 1354 Planarity : 0.004 0.046 1522 Dihedral : 6.934 78.714 1251 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.06 % Allowed : 14.36 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.27), residues: 1094 helix: 1.00 (0.24), residues: 529 sheet: 0.66 (0.51), residues: 111 loop : -0.65 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 204 HIS 0.002 0.000 HIS A 299 PHE 0.019 0.001 PHE A 183 TYR 0.009 0.001 TYR B 274 ARG 0.007 0.000 ARG E 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3294.27 seconds wall clock time: 59 minutes 50.95 seconds (3590.95 seconds total)