Starting phenix.real_space_refine on Thu Sep 26 11:41:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w18_21503/09_2024/6w18_21503.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w18_21503/09_2024/6w18_21503.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/6w18_21503/09_2024/6w18_21503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w18_21503/09_2024/6w18_21503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w18_21503/09_2024/6w18_21503.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w18_21503/09_2024/6w18_21503.cif" } resolution = 4.2 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= 0.009 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 41 5.16 5 C 8327 2.51 5 N 2310 2.21 5 O 2466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13151 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2624 Classifications: {'peptide': 370} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 88} Link IDs: {'PTRANS': 18, 'TRANS': 351} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 191 Chain: "B" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2405 Classifications: {'peptide': 367} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 156} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 553 Unresolved non-hydrogen angles: 691 Unresolved non-hydrogen dihedrals: 448 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 16, 'PHE:plan': 6, 'GLU:plan': 20, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 307 Chain: "C" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2592 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2415 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 280} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 972 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 12, 'TRANS': 161} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 577 Unresolved non-hydrogen dihedrals: 386 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 8, 'GLU:plan': 8, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 249 Chain: "F" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1357 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 723 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 322 Unresolved non-hydrogen angles: 419 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 184 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.04, per 1000 atoms: 0.61 Number of scatterers: 13151 At special positions: 0 Unit cell: (98.0784, 142.739, 143.615, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 6 15.00 Mg 1 11.99 O 2466 8.00 N 2310 7.00 C 8327 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 - 3.00 Amino acid : True - 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: 3.41 Conformation dependent library (CDL) restraints added in 2.0 seconds 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3464 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 20 sheets defined 41.7% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 77 through 84 Processing helix chain 'A' and resid 101 through 115 removed outlier: 3.815A pdb=" N ARG A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.948A pdb=" N HIS A 124 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.681A pdb=" N THR A 170 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 223 removed outlier: 3.709A pdb=" N VAL A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 242 Processing helix chain 'A' and resid 250 through 260 removed outlier: 3.582A pdb=" N SER A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 295 Proline residue: A 290 - end of helix removed outlier: 4.364A pdb=" N PHE A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.983A pdb=" N ALA A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 318 removed outlier: 4.059A pdb=" N SER A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 327 removed outlier: 4.369A pdb=" N GLY A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 354 through 366 removed outlier: 4.306A pdb=" N ARG A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET A 363 " --> pdb=" O HIS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.544A pdb=" N LEU A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 removed outlier: 4.102A pdb=" N GLY A 400 " --> pdb=" O PRO A 397 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A 402 " --> pdb=" O PHE A 399 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 403 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 removed outlier: 4.226A pdb=" N GLU A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.809A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 181 through 196 Processing helix chain 'B' and resid 207 through 217 Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.655A pdb=" N HIS B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.838A pdb=" N TYR B 255 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 257 No H-bonds generated for 'chain 'B' and resid 256 through 257' Processing helix chain 'B' and resid 258 through 263 removed outlier: 4.353A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 273 through 283 removed outlier: 3.691A pdb=" N ILE B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.554A pdb=" N ARG B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.811A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 323 Processing helix chain 'B' and resid 348 through 359 removed outlier: 3.974A pdb=" N ASP B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 removed outlier: 4.382A pdb=" N GLN B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN B 364 " --> pdb=" O ILE B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 359 through 364' Processing helix chain 'D' and resid 8 through 21 removed outlier: 3.670A pdb=" N THR D 16 " --> pdb=" O TYR D 12 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 64 Processing helix chain 'D' and resid 67 through 76 removed outlier: 3.845A pdb=" N LEU D 71 " --> pdb=" O THR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 119 removed outlier: 5.417A pdb=" N LYS D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ARG D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 137 removed outlier: 4.123A pdb=" N ARG D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 151 removed outlier: 3.690A pdb=" N LEU D 147 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 204 removed outlier: 4.040A pdb=" N ARG D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 210 removed outlier: 6.126A pdb=" N ALA D 208 " --> pdb=" O ARG D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 228 removed outlier: 4.145A pdb=" N ASP D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 Processing helix chain 'D' and resid 252 through 255 removed outlier: 3.590A pdb=" N ARG D 255 " --> pdb=" O PRO D 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 255' Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.980A pdb=" N SER D 260 " --> pdb=" O GLU D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 298 removed outlier: 3.779A pdb=" N LEU D 269 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N HIS D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 55 removed outlier: 3.545A pdb=" N GLU E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE E 48 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY E 49 " --> pdb=" O ASP E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 84 removed outlier: 3.787A pdb=" N ARG E 68 " --> pdb=" O GLY E 64 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 101 Processing helix chain 'E' and resid 113 through 118 Processing helix chain 'E' and resid 126 through 150 removed outlier: 3.575A pdb=" N TYR E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 164 removed outlier: 3.550A pdb=" N THR E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 172 Processing helix chain 'F' and resid 4 through 20 removed outlier: 3.970A pdb=" N TYR F 8 " --> pdb=" O THR F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 97 removed outlier: 3.829A pdb=" N ARG F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 126 removed outlier: 3.627A pdb=" N MET F 126 " --> pdb=" O HIS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 166 removed outlier: 3.930A pdb=" N LEU F 131 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE F 136 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN F 154 " --> pdb=" O LYS F 150 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY F 155 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG F 156 " --> pdb=" O PHE F 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 31 Processing helix chain 'G' and resid 34 through 47 Proline residue: G 41 - end of helix Processing helix chain 'G' and resid 54 through 60 removed outlier: 3.974A pdb=" N THR G 58 " --> pdb=" O GLN G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 86 Processing helix chain 'G' and resid 92 through 98 Processing helix chain 'G' and resid 100 through 115 Processing helix chain 'G' and resid 123 through 137 Processing helix chain 'G' and resid 140 through 147 removed outlier: 3.660A pdb=" N ASN G 147 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 4.342A pdb=" N PHE A 31 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 19 " --> pdb=" O TYR A 29 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A 29 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 removed outlier: 3.534A pdb=" N PHE A 75 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 3.859A pdb=" N ARG A 95 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 201 removed outlier: 3.566A pdb=" N VAL A 183 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 181 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N THR A 182 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER A 333 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 184 " --> pdb=" O SER A 333 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 7 through 9 removed outlier: 3.559A pdb=" N VAL B 7 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS B 16 " --> pdb=" O ASP B 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 105 through 107 removed outlier: 6.756A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 153 through 155 Processing sheet with id=AA8, first strand: chain 'B' and resid 165 through 166 Processing sheet with id=AA9, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.525A pdb=" N ARG B 238 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B 250 " --> pdb=" O ARG B 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.568A pdb=" N THR C 28 " --> pdb=" O GLU C 36 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU C 36 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL C 35 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR C 50 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU C 37 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 58 through 62 removed outlier: 4.155A pdb=" N CYS C 60 " --> pdb=" O CYS C 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 103 through 108 removed outlier: 3.802A pdb=" N PHE C 105 " --> pdb=" O GLY C 118 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS C 127 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER C 125 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.551A pdb=" N TYR C 202 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 211 through 212 Processing sheet with id=AB7, first strand: chain 'C' and resid 265 through 267 removed outlier: 3.855A pdb=" N ALA C 267 " --> pdb=" O ILE C 275 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 347 through 352 removed outlier: 4.982A pdb=" N SER C 366 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU C 350 " --> pdb=" O THR C 364 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR C 364 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY C 367 " --> pdb=" O ARG C 371 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 41 through 42 removed outlier: 3.635A pdb=" N SER D 42 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 157 through 159 removed outlier: 3.690A pdb=" N MET D 157 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 169 " --> pdb=" O MET D 157 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL D 168 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL D 179 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP D 170 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR D 177 " --> pdb=" O TRP D 170 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL D 241 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR D 242 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 51 through 53 removed outlier: 3.639A pdb=" N SER F 73 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU F 64 " --> pdb=" O ARG F 71 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE F 72 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE F 74 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE F 114 " --> pdb=" O ILE F 74 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1467 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: 3.74 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4448 1.34 - 1.46: 2957 1.46 - 1.58: 5940 1.58 - 1.69: 10 1.69 - 1.81: 64 Bond restraints: 13419 Sorted by residual: bond pdb=" O5' ATP A 501 " pdb=" PA ATP A 501 " ideal model delta sigma weight residual 1.579 1.604 -0.025 1.10e-02 8.26e+03 5.14e+00 bond pdb=" O5' ATP B 401 " pdb=" PA ATP B 401 " ideal model delta sigma weight residual 1.579 1.603 -0.024 1.10e-02 8.26e+03 4.90e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" O2B ATP B 401 " pdb=" PB ATP B 401 " ideal model delta sigma weight residual 1.529 1.493 0.036 2.20e-02 2.07e+03 2.70e+00 bond pdb=" O2B ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 1.529 1.493 0.036 2.20e-02 2.07e+03 2.63e+00 ... (remaining 13414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 18108 1.45 - 2.90: 155 2.90 - 4.35: 63 4.35 - 5.80: 5 5.80 - 7.25: 2 Bond angle restraints: 18333 Sorted by residual: angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 132.62 7.25 1.00e+00 1.00e+00 5.25e+01 angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 132.69 7.18 1.00e+00 1.00e+00 5.16e+01 angle pdb=" PA ATP B 401 " pdb=" O3A ATP B 401 " pdb=" PB ATP B 401 " ideal model delta sigma weight residual 136.83 132.51 4.32 1.00e+00 1.00e+00 1.86e+01 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 132.58 4.25 1.00e+00 1.00e+00 1.80e+01 angle pdb=" N VAL F 38 " pdb=" CA VAL F 38 " pdb=" C VAL F 38 " ideal model delta sigma weight residual 113.47 109.82 3.65 1.01e+00 9.80e-01 1.31e+01 ... (remaining 18328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 7454 17.45 - 34.90: 378 34.90 - 52.35: 84 52.35 - 69.81: 17 69.81 - 87.26: 7 Dihedral angle restraints: 7940 sinusoidal: 2593 harmonic: 5347 Sorted by residual: dihedral pdb=" CB GLU C 16 " pdb=" CG GLU C 16 " pdb=" CD GLU C 16 " pdb=" OE1 GLU C 16 " ideal model delta sinusoidal sigma weight residual 0.00 87.26 -87.26 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB MET F 149 " pdb=" CG MET F 149 " pdb=" SD MET F 149 " pdb=" CE MET F 149 " ideal model delta sinusoidal sigma weight residual 60.00 119.04 -59.04 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 363 " pdb=" CG MET A 363 " pdb=" SD MET A 363 " pdb=" CE MET A 363 " ideal model delta sinusoidal sigma weight residual 180.00 -129.53 -50.47 3 1.50e+01 4.44e-03 8.90e+00 ... (remaining 7937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1445 0.032 - 0.063: 422 0.063 - 0.095: 133 0.095 - 0.126: 112 0.126 - 0.158: 4 Chirality restraints: 2116 Sorted by residual: chirality pdb=" C3' ATP B 401 " pdb=" C2' ATP B 401 " pdb=" C4' ATP B 401 " pdb=" O3' ATP B 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.79 0.16 2.00e-01 2.50e+01 6.25e-01 chirality pdb=" C3' ATP A 501 " pdb=" C2' ATP A 501 " pdb=" C4' ATP A 501 " pdb=" O3' ATP A 501 " both_signs ideal model delta sigma weight residual False -2.63 -2.79 0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" C2' ATP A 501 " pdb=" C1' ATP A 501 " pdb=" C3' ATP A 501 " pdb=" O2' ATP A 501 " both_signs ideal model delta sigma weight residual False -2.68 -2.54 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 2113 not shown) Planarity restraints: 2404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 155 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO C 156 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 156 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 156 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 307 " -0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO A 308 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 322 " 0.006 2.00e-02 2.50e+03 6.70e-03 7.85e-01 pdb=" CG PHE B 322 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE B 322 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 322 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 322 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 322 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 322 " 0.001 2.00e-02 2.50e+03 ... (remaining 2401 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 909 2.74 - 3.28: 13463 3.28 - 3.82: 19747 3.82 - 4.36: 21410 4.36 - 4.90: 38550 Nonbonded interactions: 94079 Sorted by model distance: nonbonded pdb=" O LEU B 229 " pdb=" OG1 THR B 233 " model vdw 2.196 3.040 nonbonded pdb=" NH1 ARG C 146 " pdb=" OH TYR C 171 " model vdw 2.211 3.120 nonbonded pdb=" OE1 GLU F 24 " pdb=" ND2 ASN F 120 " model vdw 2.262 3.120 nonbonded pdb=" O THR A 14 " pdb=" O3G ATP A 501 " model vdw 2.267 3.040 nonbonded pdb=" O GLU D 247 " pdb=" OG1 THR D 251 " model vdw 2.273 3.040 ... (remaining 94074 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 max=1.00 mean=0.98 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.650 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 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 : 0.002 0.036 13419 Z= 0.117 Angle : 0.412 7.246 18333 Z= 0.245 Chirality : 0.040 0.158 2116 Planarity : 0.002 0.042 2404 Dihedral : 11.721 87.256 4476 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.18), residues: 1807 helix: -0.42 (0.20), residues: 634 sheet: -3.42 (0.27), residues: 221 loop : -3.44 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 45 HIS 0.001 0.000 HIS C 8 PHE 0.015 0.000 PHE B 322 TYR 0.003 0.000 TYR A 246 ARG 0.002 0.000 ARG F 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 1.529 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: A 337 THR cc_start: 0.8468 (p) cc_final: 0.8264 (p) REVERT: A 362 GLU cc_start: 0.7101 (tt0) cc_final: 0.6668 (mm-30) REVERT: A 373 ASP cc_start: 0.5645 (m-30) cc_final: 0.5159 (t0) REVERT: A 408 ASP cc_start: 0.5975 (m-30) cc_final: 0.5638 (t0) REVERT: B 19 TYR cc_start: 0.4779 (m-10) cc_final: 0.4295 (t80) REVERT: B 87 ASP cc_start: 0.6840 (t0) cc_final: 0.5821 (m-30) REVERT: B 165 VAL cc_start: 0.7147 (t) cc_final: 0.6930 (m) REVERT: B 229 LEU cc_start: 0.8602 (mp) cc_final: 0.8213 (tp) REVERT: B 363 GLN cc_start: 0.6565 (pm20) cc_final: 0.6058 (mp10) REVERT: C 8 HIS cc_start: 0.5463 (m170) cc_final: 0.5147 (m-70) REVERT: C 9 ILE cc_start: 0.7652 (mm) cc_final: 0.7397 (pt) REVERT: D 1 MET cc_start: 0.5289 (ptp) cc_final: 0.4959 (ptt) REVERT: D 27 ILE cc_start: 0.7818 (mt) cc_final: 0.6962 (mp) REVERT: D 84 MET cc_start: 0.5121 (pmm) cc_final: 0.4893 (pmm) REVERT: D 161 TYR cc_start: 0.7362 (p90) cc_final: 0.7102 (p90) REVERT: D 257 ASP cc_start: 0.7059 (p0) cc_final: 0.6854 (p0) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.2728 time to fit residues: 142.4103 Evaluate side-chains 202 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 73 optimal weight: 0.2980 chunk 141 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 379 HIS B 327 HIS ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 278 GLN C 343 HIS D 124 HIS D 160 HIS D 249 HIS ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13419 Z= 0.237 Angle : 0.596 6.205 18333 Z= 0.316 Chirality : 0.046 0.212 2116 Planarity : 0.004 0.052 2404 Dihedral : 5.280 83.157 2021 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.18 % Allowed : 5.49 % Favored : 94.33 % 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: -2.32 (0.19), residues: 1807 helix: 0.40 (0.21), residues: 638 sheet: -2.57 (0.30), residues: 222 loop : -2.78 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 321 HIS 0.006 0.001 HIS A 379 PHE 0.035 0.002 PHE D 265 TYR 0.017 0.002 TYR B 255 ARG 0.007 0.001 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 260 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 GLN cc_start: 0.8365 (mp10) cc_final: 0.8072 (mp10) REVERT: A 337 THR cc_start: 0.8660 (p) cc_final: 0.8372 (p) REVERT: A 373 ASP cc_start: 0.6051 (m-30) cc_final: 0.5407 (t0) REVERT: A 408 ASP cc_start: 0.6480 (m-30) cc_final: 0.6243 (m-30) REVERT: B 71 MET cc_start: 0.5019 (mtp) cc_final: 0.4497 (ttm) REVERT: B 165 VAL cc_start: 0.7777 (t) cc_final: 0.7468 (m) REVERT: B 363 GLN cc_start: 0.7010 (pm20) cc_final: 0.6245 (mp10) REVERT: D 109 MET cc_start: 0.9169 (mmm) cc_final: 0.8894 (mmt) REVERT: F 159 LEU cc_start: 0.8950 (tp) cc_final: 0.8618 (tp) outliers start: 2 outliers final: 1 residues processed: 262 average time/residue: 0.2380 time to fit residues: 89.5472 Evaluate side-chains 178 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 136 optimal weight: 20.0000 chunk 111 optimal weight: 6.9990 chunk 45 optimal weight: 30.0000 chunk 164 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS C 133 ASN C 278 GLN D 160 HIS E 97 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 13419 Z= 0.337 Angle : 0.693 7.832 18333 Z= 0.367 Chirality : 0.049 0.178 2116 Planarity : 0.005 0.055 2404 Dihedral : 5.826 69.853 2021 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.35 % Allowed : 6.82 % Favored : 92.83 % 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: -2.39 (0.19), residues: 1807 helix: 0.12 (0.21), residues: 640 sheet: -2.48 (0.31), residues: 230 loop : -2.67 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 321 HIS 0.011 0.002 HIS C 343 PHE 0.033 0.003 PHE C 115 TYR 0.018 0.002 TYR F 121 ARG 0.011 0.001 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 216 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: A 90 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7821 (pp) REVERT: A 408 ASP cc_start: 0.6787 (m-30) cc_final: 0.6559 (m-30) REVERT: B 165 VAL cc_start: 0.8341 (t) cc_final: 0.8001 (p) REVERT: B 363 GLN cc_start: 0.7367 (pm20) cc_final: 0.6642 (mp10) REVERT: B 380 ARG cc_start: 0.7181 (mmp80) cc_final: 0.6808 (mmp80) REVERT: C 278 GLN cc_start: 0.6351 (mm110) cc_final: 0.6017 (mp10) REVERT: D 82 PRO cc_start: 0.7509 (Cg_exo) cc_final: 0.7192 (Cg_endo) REVERT: D 163 ASP cc_start: 0.7552 (p0) cc_final: 0.7338 (p0) REVERT: D 257 ASP cc_start: 0.7461 (p0) cc_final: 0.7193 (p0) REVERT: D 280 MET cc_start: 0.7628 (mmm) cc_final: 0.6901 (mmp) REVERT: F 159 LEU cc_start: 0.8987 (tp) cc_final: 0.8765 (tp) outliers start: 4 outliers final: 1 residues processed: 219 average time/residue: 0.2506 time to fit residues: 79.7547 Evaluate side-chains 159 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 174 optimal weight: 0.1980 chunk 86 optimal weight: 4.9990 chunk 156 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS D 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13419 Z= 0.208 Angle : 0.584 9.041 18333 Z= 0.304 Chirality : 0.045 0.173 2116 Planarity : 0.004 0.053 2404 Dihedral : 5.329 67.227 2021 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % 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: -1.99 (0.20), residues: 1807 helix: 0.44 (0.22), residues: 640 sheet: -2.20 (0.32), residues: 238 loop : -2.43 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 387 HIS 0.008 0.001 HIS B 327 PHE 0.019 0.002 PHE B 322 TYR 0.015 0.001 TYR B 221 ARG 0.007 0.001 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 TYR cc_start: 0.7029 (m-10) cc_final: 0.6524 (t80) REVERT: A 287 PHE cc_start: 0.7246 (m-80) cc_final: 0.6830 (m-80) REVERT: A 316 GLN cc_start: 0.8108 (mp10) cc_final: 0.7811 (mp10) REVERT: A 337 THR cc_start: 0.8644 (p) cc_final: 0.8428 (p) REVERT: A 408 ASP cc_start: 0.6826 (m-30) cc_final: 0.6584 (m-30) REVERT: B 165 VAL cc_start: 0.8232 (t) cc_final: 0.7920 (p) REVERT: B 363 GLN cc_start: 0.7289 (pm20) cc_final: 0.6597 (mp10) REVERT: B 380 ARG cc_start: 0.7192 (mmp80) cc_final: 0.6840 (mmp80) REVERT: C 101 ARG cc_start: 0.8521 (mpt180) cc_final: 0.8181 (mmp-170) REVERT: D 257 ASP cc_start: 0.7354 (p0) cc_final: 0.7017 (p0) REVERT: F 159 LEU cc_start: 0.8889 (tp) cc_final: 0.8513 (tp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2640 time to fit residues: 84.8357 Evaluate side-chains 166 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 157 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS B 348 HIS C 345 ASN D 160 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13419 Z= 0.213 Angle : 0.592 10.587 18333 Z= 0.310 Chirality : 0.045 0.163 2116 Planarity : 0.004 0.053 2404 Dihedral : 5.347 68.956 2021 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.20), residues: 1807 helix: 0.48 (0.21), residues: 645 sheet: -2.18 (0.31), residues: 243 loop : -2.30 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 387 HIS 0.016 0.001 HIS B 327 PHE 0.020 0.001 PHE B 322 TYR 0.017 0.001 TYR D 161 ARG 0.008 0.001 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.5978 (tmtt) cc_final: 0.5630 (tmtt) REVERT: A 88 TYR cc_start: 0.7038 (m-10) cc_final: 0.6503 (t80) REVERT: A 107 ARG cc_start: 0.7303 (mtp85) cc_final: 0.6901 (mtt180) REVERT: A 169 TRP cc_start: 0.8590 (m-10) cc_final: 0.7826 (m-10) REVERT: A 316 GLN cc_start: 0.8056 (mp10) cc_final: 0.7852 (mp10) REVERT: A 408 ASP cc_start: 0.7036 (m-30) cc_final: 0.6681 (m-30) REVERT: B 165 VAL cc_start: 0.8312 (t) cc_final: 0.7990 (p) REVERT: B 363 GLN cc_start: 0.7364 (pm20) cc_final: 0.6620 (mp10) REVERT: C 101 ARG cc_start: 0.8549 (mpt180) cc_final: 0.8286 (mmp-170) REVERT: D 257 ASP cc_start: 0.7466 (p0) cc_final: 0.7105 (p0) REVERT: F 159 LEU cc_start: 0.8904 (tp) cc_final: 0.8531 (tp) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2572 time to fit residues: 82.5842 Evaluate side-chains 166 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 57 optimal weight: 0.2980 chunk 91 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS C 47 HIS D 160 HIS D 173 HIS E 97 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.6294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13419 Z= 0.308 Angle : 0.673 11.215 18333 Z= 0.356 Chirality : 0.048 0.184 2116 Planarity : 0.005 0.052 2404 Dihedral : 5.953 75.055 2021 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.18 % Allowed : 2.83 % Favored : 96.99 % 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: -2.13 (0.20), residues: 1807 helix: 0.19 (0.21), residues: 654 sheet: -2.30 (0.30), residues: 257 loop : -2.42 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 387 HIS 0.010 0.002 HIS B 327 PHE 0.029 0.002 PHE A 147 TYR 0.017 0.002 TYR B 221 ARG 0.005 0.001 ARG F 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LYS cc_start: 0.6212 (tmtt) cc_final: 0.5616 (tmtt) REVERT: A 316 GLN cc_start: 0.7975 (mp10) cc_final: 0.7774 (mp10) REVERT: B 363 GLN cc_start: 0.7535 (pm20) cc_final: 0.6839 (mp10) REVERT: C 101 ARG cc_start: 0.8552 (mpt180) cc_final: 0.8277 (mmp-170) REVERT: D 206 ARG cc_start: 0.7272 (mpp80) cc_final: 0.7029 (mpp80) REVERT: D 257 ASP cc_start: 0.7475 (p0) cc_final: 0.6984 (p0) REVERT: F 159 LEU cc_start: 0.8974 (tp) cc_final: 0.8618 (tp) outliers start: 2 outliers final: 0 residues processed: 205 average time/residue: 0.2464 time to fit residues: 73.9773 Evaluate side-chains 162 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 chunk 97 optimal weight: 0.7980 chunk 174 optimal weight: 20.0000 chunk 109 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS D 160 HIS E 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.6354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13419 Z= 0.230 Angle : 0.616 9.509 18333 Z= 0.321 Chirality : 0.046 0.164 2116 Planarity : 0.005 0.054 2404 Dihedral : 5.685 75.642 2021 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.18 % Allowed : 2.04 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.20), residues: 1807 helix: 0.41 (0.21), residues: 646 sheet: -2.24 (0.30), residues: 267 loop : -2.17 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 387 HIS 0.008 0.001 HIS B 327 PHE 0.018 0.002 PHE B 322 TYR 0.019 0.002 TYR D 161 ARG 0.016 0.001 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 203 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: A 83 LYS cc_start: 0.6169 (tmtt) cc_final: 0.5951 (tmtt) REVERT: A 105 MET cc_start: 0.8668 (tpp) cc_final: 0.8416 (tpp) REVERT: A 169 TRP cc_start: 0.8622 (m-10) cc_final: 0.7738 (m-10) REVERT: B 231 GLU cc_start: 0.7694 (pm20) cc_final: 0.7480 (pm20) REVERT: B 363 GLN cc_start: 0.7487 (pm20) cc_final: 0.6821 (mp10) REVERT: C 101 ARG cc_start: 0.8549 (mpt180) cc_final: 0.8288 (mmp-170) REVERT: D 206 ARG cc_start: 0.7345 (mpp80) cc_final: 0.6999 (mpp80) REVERT: D 257 ASP cc_start: 0.7419 (p0) cc_final: 0.7025 (p0) REVERT: D 276 SER cc_start: 0.9112 (p) cc_final: 0.8805 (t) REVERT: F 159 LEU cc_start: 0.8854 (tp) cc_final: 0.8493 (tp) outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.2402 time to fit residues: 71.1377 Evaluate side-chains 156 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 0.0570 chunk 104 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 86 optimal weight: 0.2980 chunk 16 optimal weight: 10.0000 chunk 137 optimal weight: 40.0000 chunk 158 optimal weight: 1.9990 overall best weight: 1.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS E 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13419 Z= 0.191 Angle : 0.598 10.209 18333 Z= 0.310 Chirality : 0.045 0.162 2116 Planarity : 0.004 0.054 2404 Dihedral : 5.466 73.675 2021 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.18 % Allowed : 1.77 % Favored : 98.05 % 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: -1.59 (0.20), residues: 1807 helix: 0.62 (0.22), residues: 639 sheet: -2.06 (0.31), residues: 258 loop : -2.02 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 284 HIS 0.019 0.001 HIS B 327 PHE 0.025 0.001 PHE A 147 TYR 0.012 0.001 TYR B 188 ARG 0.011 0.001 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 205 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 TYR cc_start: 0.7071 (m-10) cc_final: 0.6080 (t80) REVERT: A 169 TRP cc_start: 0.8569 (m-10) cc_final: 0.7717 (m-10) REVERT: A 287 PHE cc_start: 0.7371 (m-80) cc_final: 0.7124 (m-80) REVERT: A 337 THR cc_start: 0.8625 (p) cc_final: 0.8381 (p) REVERT: B 231 GLU cc_start: 0.7677 (pm20) cc_final: 0.7455 (pm20) REVERT: B 363 GLN cc_start: 0.7472 (pm20) cc_final: 0.6832 (mp10) REVERT: C 101 ARG cc_start: 0.8554 (mpt180) cc_final: 0.8273 (mmp-170) REVERT: D 82 PRO cc_start: 0.7986 (Cg_exo) cc_final: 0.7656 (Cg_endo) REVERT: D 206 ARG cc_start: 0.7417 (mpp80) cc_final: 0.7054 (mpp80) REVERT: D 257 ASP cc_start: 0.7387 (p0) cc_final: 0.6957 (p0) REVERT: F 159 LEU cc_start: 0.8842 (tp) cc_final: 0.8563 (tp) outliers start: 2 outliers final: 0 residues processed: 206 average time/residue: 0.2318 time to fit residues: 70.6601 Evaluate side-chains 158 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 0.5980 chunk 152 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS E 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.6816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13419 Z= 0.314 Angle : 0.700 10.739 18333 Z= 0.370 Chirality : 0.048 0.182 2116 Planarity : 0.005 0.058 2404 Dihedral : 6.200 81.576 2021 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 0.18 % Allowed : 1.06 % Favored : 98.76 % 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: -1.96 (0.20), residues: 1807 helix: 0.23 (0.21), residues: 663 sheet: -2.26 (0.30), residues: 267 loop : -2.23 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 284 HIS 0.019 0.002 HIS B 327 PHE 0.023 0.002 PHE B 322 TYR 0.020 0.002 TYR C 233 ARG 0.014 0.001 ARG C 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 199 time to evaluate : 1.570 Fit side-chains revert: symmetry clash REVERT: A 88 TYR cc_start: 0.7182 (m-10) cc_final: 0.6086 (t80) REVERT: A 287 PHE cc_start: 0.7497 (m-80) cc_final: 0.7105 (m-80) REVERT: A 316 GLN cc_start: 0.7984 (mp10) cc_final: 0.7680 (mp10) REVERT: B 363 GLN cc_start: 0.7671 (pm20) cc_final: 0.7031 (mp10) REVERT: C 101 ARG cc_start: 0.8503 (mpt180) cc_final: 0.8228 (mmp-170) REVERT: D 257 ASP cc_start: 0.7388 (p0) cc_final: 0.7025 (p0) REVERT: D 276 SER cc_start: 0.9067 (p) cc_final: 0.8825 (t) REVERT: F 159 LEU cc_start: 0.8875 (tp) cc_final: 0.8500 (tp) outliers start: 2 outliers final: 0 residues processed: 200 average time/residue: 0.2349 time to fit residues: 69.0412 Evaluate side-chains 159 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 165 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS C 43 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS E 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.6846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13419 Z= 0.235 Angle : 0.663 12.586 18333 Z= 0.344 Chirality : 0.046 0.203 2116 Planarity : 0.005 0.054 2404 Dihedral : 5.909 78.954 2021 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.27 % Allowed : 0.35 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.20), residues: 1807 helix: 0.37 (0.21), residues: 653 sheet: -2.11 (0.31), residues: 251 loop : -2.17 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 284 HIS 0.019 0.002 HIS B 327 PHE 0.016 0.002 PHE F 72 TYR 0.023 0.002 TYR B 221 ARG 0.012 0.001 ARG C 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 196 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 PHE cc_start: 0.7423 (m-80) cc_final: 0.7023 (m-80) REVERT: A 316 GLN cc_start: 0.7955 (mp10) cc_final: 0.7640 (mp10) REVERT: B 363 GLN cc_start: 0.7622 (pm20) cc_final: 0.7027 (mp10) REVERT: C 101 ARG cc_start: 0.8518 (mpt180) cc_final: 0.8179 (mmp-170) REVERT: D 257 ASP cc_start: 0.7396 (p0) cc_final: 0.6979 (p0) REVERT: D 276 SER cc_start: 0.9025 (p) cc_final: 0.8792 (t) REVERT: F 34 SER cc_start: 0.8413 (p) cc_final: 0.8164 (p) REVERT: F 150 LYS cc_start: 0.8759 (ttmm) cc_final: 0.8508 (ttmm) REVERT: F 159 LEU cc_start: 0.8832 (tp) cc_final: 0.8605 (tp) outliers start: 3 outliers final: 0 residues processed: 198 average time/residue: 0.2437 time to fit residues: 70.1893 Evaluate side-chains 157 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 147 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 126 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.155385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.136244 restraints weight = 26713.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.135334 restraints weight = 33636.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136816 restraints weight = 26160.426| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.6698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13419 Z= 0.160 Angle : 0.608 12.526 18333 Z= 0.310 Chirality : 0.045 0.200 2116 Planarity : 0.004 0.054 2404 Dihedral : 5.433 70.749 2021 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.21), residues: 1807 helix: 0.70 (0.22), residues: 639 sheet: -1.90 (0.32), residues: 246 loop : -1.90 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 387 HIS 0.018 0.001 HIS B 327 PHE 0.032 0.001 PHE A 147 TYR 0.019 0.001 TYR C 233 ARG 0.009 0.001 ARG C 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2570.72 seconds wall clock time: 46 minutes 24.11 seconds (2784.11 seconds total)