Starting phenix.real_space_refine on Sat Mar 16 00:14:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w18_21503/03_2024/6w18_21503_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w18_21503/03_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_21503/03_2024/6w18_21503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w18_21503/03_2024/6w18_21503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w18_21503/03_2024/6w18_21503_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w18_21503/03_2024/6w18_21503_updated.pdb" } 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 Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "C GLU 36": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 242": "NH1" <-> "NH2" Residue "C ARG 255": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D ARG 138": "NH1" <-> "NH2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D GLU 247": "OE1" <-> "OE2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D ARG 255": "NH1" <-> "NH2" Residue "D ARG 297": "NH1" <-> "NH2" Residue "F ARG 6": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ARG 42": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F ARG 97": "NH1" <-> "NH2" Residue "F ARG 106": "NH1" <-> "NH2" Residue "F ARG 158": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: 7.18, per 1000 atoms: 0.55 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 - 3.50 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: 5.39 Conformation dependent library (CDL) restraints added in 2.5 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... running ksdssp... Secondary structure from input PDB file: 64 helices and 15 sheets defined 35.8% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'A' and resid 78 through 85 removed outlier: 5.890A pdb=" N SER A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 114 removed outlier: 3.815A pdb=" N ARG A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 160 through 170 removed outlier: 3.694A pdb=" N ALA A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TRP A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.505A pdb=" N LEU A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.582A pdb=" N SER A 256 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 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 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 320 through 326 removed outlier: 4.369A pdb=" N GLY A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 355 through 365 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 388 through 394 removed outlier: 3.544A pdb=" N LEU A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 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) Processing helix chain 'A' and resid 407 through 410 No H-bonds generated for 'chain 'A' and resid 407 through 410' Processing helix chain 'B' and resid 55 through 59 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 removed outlier: 4.089A pdb=" N GLN B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 223 through 232 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 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.691A pdb=" N ILE B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 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) removed outlier: 4.471A pdb=" N ARG B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 296 " --> pdb=" O TYR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 360 through 363 No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'D' and resid 9 through 20 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 63 Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 103 through 136 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) removed outlier: 3.959A pdb=" N ALA D 121 " --> pdb=" O ASN D 117 " (cutoff:3.500A) Proline residue: D 122 - end of helix 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 144 through 150 Processing helix chain 'D' and resid 187 through 205 removed outlier: 4.040A pdb=" N ARG D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ARG D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 224 through 227 No H-bonds generated for 'chain 'D' and resid 224 through 227' Processing helix chain 'D' and resid 247 through 250 No H-bonds generated for 'chain 'D' and resid 247 through 250' Processing helix chain 'D' and resid 252 through 254 No H-bonds generated for 'chain 'D' and resid 252 through 254' Processing helix chain 'D' and resid 257 through 298 removed outlier: 3.951A pdb=" N VAL D 264 " --> pdb=" O SER D 260 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE D 265 " --> pdb=" O HIS D 261 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ARG D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASN D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) 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 43 through 54 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 65 through 83 removed outlier: 3.742A pdb=" N LEU E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 100 Processing helix chain 'E' and resid 114 through 117 No H-bonds generated for 'chain 'E' and resid 114 through 117' Processing helix chain 'E' and resid 127 through 149 Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 169 through 171 No H-bonds generated for 'chain 'E' and resid 169 through 171' Processing helix chain 'F' and resid 5 through 19 Processing helix chain 'F' and resid 81 through 96 Processing helix chain 'F' and resid 120 through 125 Processing helix chain 'F' and resid 128 through 165 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 27 through 30 No H-bonds generated for 'chain 'G' and resid 27 through 30' Processing helix chain 'G' and resid 35 through 46 Proline residue: G 41 - end of helix Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 71 through 85 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 101 through 116 removed outlier: 3.897A pdb=" N ALA G 116 " --> pdb=" O TYR G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 136 Processing helix chain 'G' and resid 141 through 146 Processing sheet with id= A, first strand: chain 'A' and resid 16 through 19 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= B, first strand: chain 'A' and resid 191 through 196 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: 7.015A pdb=" N VAL A 331 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N SER A 186 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER A 333 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing sheet with id= C, 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= D, first strand: chain 'B' and resid 105 through 107 removed outlier: 3.932A pdb=" N GLU B 107 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 153 through 155 Processing sheet with id= F, 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= G, 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: 5.550A pdb=" N GLU C 39 " --> pdb=" O HIS C 47 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N HIS C 47 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASP C 41 " --> pdb=" O TRP C 45 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TRP C 45 " --> pdb=" O ASP C 41 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 70 through 73 Processing sheet with id= I, first strand: chain 'C' and resid 106 through 108 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= J, first strand: chain 'C' and resid 220 through 223 Processing sheet with id= K, 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= L, first strand: chain 'C' and resid 350 through 352 Processing sheet with id= M, first strand: chain 'D' and resid 50 through 52 Processing sheet with id= N, 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= O, first strand: chain 'F' and resid 51 through 53 removed outlier: 3.860A pdb=" N GLN F 60 " --> pdb=" O ARG F 75 " (cutoff:3.500A) 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) 426 hydrogen bonds defined for protein. 1212 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: 3.21 Time building geometry restraints manager: 5.80 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: 99.55 - 106.43: 380 106.43 - 113.32: 7253 113.32 - 120.20: 4507 120.20 - 127.09: 6040 127.09 - 133.97: 153 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: 915 2.74 - 3.28: 13548 3.28 - 3.82: 19878 3.82 - 4.36: 21574 4.36 - 4.90: 38556 Nonbonded interactions: 94471 Sorted by model distance: nonbonded pdb=" O LEU B 229 " pdb=" OG1 THR B 233 " model vdw 2.196 2.440 nonbonded pdb=" NH1 ARG C 146 " pdb=" OH TYR C 171 " model vdw 2.211 2.520 nonbonded pdb=" O PHE C 105 " pdb=" N GLY C 118 " model vdw 2.244 2.520 nonbonded pdb=" OE1 GLU F 24 " pdb=" ND2 ASN F 120 " model vdw 2.262 2.520 nonbonded pdb=" O THR A 14 " pdb=" O3G ATP A 501 " model vdw 2.267 3.040 ... (remaining 94466 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=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: 0.760 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: 4.040 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 36.960 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.260 ------------------------------------------------------------------------------- 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= 0.121 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 : 1.705 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: 0.2697 time to fit residues: 140.4823 Evaluate side-chains 202 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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: 1.9990 chunk 46 optimal weight: 0.0070 chunk 92 optimal weight: 0.6980 chunk 73 optimal weight: 0.2980 chunk 141 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS B 327 HIS C 209 HIS C 239 GLN C 278 GLN D 124 HIS D 160 HIS D 249 HIS ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13419 Z= 0.151 Angle : 0.493 6.635 18333 Z= 0.253 Chirality : 0.043 0.189 2116 Planarity : 0.003 0.042 2404 Dihedral : 5.119 85.635 2021 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: -2.24 (0.19), residues: 1807 helix: 0.55 (0.21), residues: 631 sheet: -2.77 (0.30), residues: 214 loop : -2.71 (0.18), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 387 HIS 0.005 0.001 HIS D 261 PHE 0.019 0.001 PHE A 75 TYR 0.012 0.001 TYR B 255 ARG 0.005 0.000 ARG C 49 *********************** 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 270 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 PHE cc_start: 0.6997 (m-80) cc_final: 0.6774 (m-80) REVERT: A 316 GLN cc_start: 0.8103 (mp10) cc_final: 0.7862 (mp10) REVERT: A 337 THR cc_start: 0.8341 (p) cc_final: 0.8090 (p) REVERT: A 373 ASP cc_start: 0.5943 (m-30) cc_final: 0.5339 (t0) REVERT: A 408 ASP cc_start: 0.6264 (m-30) cc_final: 0.5996 (m-30) REVERT: B 19 TYR cc_start: 0.4891 (m-10) cc_final: 0.4141 (t80) REVERT: B 71 MET cc_start: 0.5119 (mtp) cc_final: 0.2865 (tpt) REVERT: B 87 ASP cc_start: 0.6800 (t0) cc_final: 0.5591 (m-30) REVERT: B 165 VAL cc_start: 0.7210 (t) cc_final: 0.6940 (m) REVERT: B 229 LEU cc_start: 0.8637 (mp) cc_final: 0.8437 (tp) REVERT: B 363 GLN cc_start: 0.6822 (pm20) cc_final: 0.6355 (mp10) REVERT: C 9 ILE cc_start: 0.7728 (mm) cc_final: 0.7342 (pt) REVERT: D 280 MET cc_start: 0.7382 (mmm) cc_final: 0.6034 (mmm) REVERT: F 76 ILE cc_start: 0.6932 (mt) cc_final: 0.6692 (mt) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2395 time to fit residues: 93.9739 Evaluate side-chains 189 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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: 10.0000 chunk 51 optimal weight: 0.7980 chunk 136 optimal weight: 0.0050 chunk 111 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 164 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN B 145 GLN C 278 GLN C 343 HIS D 249 HIS ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13419 Z= 0.161 Angle : 0.509 6.490 18333 Z= 0.261 Chirality : 0.044 0.162 2116 Planarity : 0.004 0.051 2404 Dihedral : 4.742 79.287 2021 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.20), residues: 1807 helix: 0.94 (0.21), residues: 635 sheet: -2.47 (0.30), residues: 248 loop : -2.34 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 387 HIS 0.005 0.001 HIS A 379 PHE 0.015 0.001 PHE A 75 TYR 0.019 0.001 TYR B 188 ARG 0.007 0.001 ARG D 185 *********************** 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 249 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 THR cc_start: 0.8607 (p) cc_final: 0.8362 (p) REVERT: A 373 ASP cc_start: 0.5916 (m-30) cc_final: 0.5396 (t0) REVERT: A 408 ASP cc_start: 0.6392 (m-30) cc_final: 0.6103 (m-30) REVERT: B 71 MET cc_start: 0.5240 (mtp) cc_final: 0.2533 (tpt) REVERT: B 165 VAL cc_start: 0.7561 (t) cc_final: 0.7173 (m) REVERT: B 229 LEU cc_start: 0.8959 (mp) cc_final: 0.8735 (mt) REVERT: B 363 GLN cc_start: 0.7002 (pm20) cc_final: 0.6387 (mp10) REVERT: C 9 ILE cc_start: 0.7974 (mm) cc_final: 0.7492 (pt) REVERT: D 82 PRO cc_start: 0.7557 (Cg_exo) cc_final: 0.7310 (Cg_endo) REVERT: D 257 ASP cc_start: 0.7353 (p0) cc_final: 0.7080 (p0) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.2300 time to fit residues: 83.4835 Evaluate side-chains 174 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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: 4.9990 chunk 123 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 174 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN C 133 ASN C 278 GLN D 267 ASN E 97 ASN F 60 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.5216 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= 0.293 Angle : 0.651 7.143 18333 Z= 0.345 Chirality : 0.048 0.170 2116 Planarity : 0.005 0.051 2404 Dihedral : 5.617 68.685 2021 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.09 % Allowed : 5.76 % Favored : 94.15 % 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: -2.01 (0.20), residues: 1807 helix: 0.52 (0.21), residues: 650 sheet: -2.40 (0.30), residues: 255 loop : -2.48 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 321 HIS 0.011 0.002 HIS C 343 PHE 0.029 0.002 PHE C 115 TYR 0.017 0.002 TYR F 121 ARG 0.009 0.001 ARG B 195 *********************** 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 215 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 GLN cc_start: 0.8389 (mp10) cc_final: 0.8121 (mp10) REVERT: A 408 ASP cc_start: 0.6843 (m-30) cc_final: 0.6594 (m-30) REVERT: B 165 VAL cc_start: 0.8034 (t) cc_final: 0.7416 (m) REVERT: B 363 GLN cc_start: 0.7467 (pm20) cc_final: 0.6586 (mp10) REVERT: B 380 ARG cc_start: 0.7096 (mmp80) cc_final: 0.6870 (mmp80) REVERT: C 346 MET cc_start: 0.7930 (ttt) cc_final: 0.7632 (ttt) REVERT: D 82 PRO cc_start: 0.7955 (Cg_exo) cc_final: 0.7606 (Cg_endo) REVERT: F 34 SER cc_start: 0.8825 (t) cc_final: 0.8603 (p) REVERT: F 120 ASN cc_start: 0.8289 (p0) cc_final: 0.7974 (p0) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.2588 time to fit residues: 78.6411 Evaluate side-chains 158 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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: 10.0000 chunk 99 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 130 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 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 5 ASN A 12 ASN ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** C 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN F 60 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13419 Z= 0.309 Angle : 0.657 9.131 18333 Z= 0.350 Chirality : 0.048 0.160 2116 Planarity : 0.005 0.046 2404 Dihedral : 5.950 76.135 2021 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 0.09 % Allowed : 4.07 % Favored : 95.84 % 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: -2.11 (0.20), residues: 1807 helix: 0.40 (0.21), residues: 644 sheet: -2.16 (0.30), residues: 257 loop : -2.59 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 387 HIS 0.015 0.002 HIS B 327 PHE 0.024 0.002 PHE B 322 TYR 0.018 0.002 TYR C 233 ARG 0.006 0.001 ARG B 195 *********************** 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 210 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 TYR cc_start: 0.7100 (m-80) cc_final: 0.6815 (t80) REVERT: A 146 MET cc_start: 0.8915 (tpp) cc_final: 0.8576 (tpp) REVERT: A 393 LEU cc_start: 0.8260 (tp) cc_final: 0.8007 (tt) REVERT: B 165 VAL cc_start: 0.8488 (t) cc_final: 0.8109 (p) REVERT: B 363 GLN cc_start: 0.7224 (pm20) cc_final: 0.6631 (mp10) REVERT: C 346 MET cc_start: 0.7922 (ttt) cc_final: 0.7636 (ttt) REVERT: D 224 LEU cc_start: 0.8255 (mm) cc_final: 0.8016 (mm) REVERT: D 257 ASP cc_start: 0.7603 (p0) cc_final: 0.7297 (p0) outliers start: 1 outliers final: 1 residues processed: 210 average time/residue: 0.2550 time to fit residues: 77.3106 Evaluate side-chains 160 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.625 ------------------------------------------------------------------------------- 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: 0.0030 chunk 157 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 102 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 overall best weight: 1.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 HIS C 278 GLN ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13419 Z= 0.185 Angle : 0.558 7.588 18333 Z= 0.289 Chirality : 0.045 0.181 2116 Planarity : 0.004 0.067 2404 Dihedral : 5.388 71.289 2021 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.09 % Allowed : 2.48 % Favored : 97.43 % 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: -1.69 (0.20), residues: 1807 helix: 0.79 (0.22), residues: 632 sheet: -2.14 (0.30), residues: 267 loop : -2.25 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 387 HIS 0.010 0.001 HIS B 327 PHE 0.016 0.001 PHE B 322 TYR 0.027 0.001 TYR B 188 ARG 0.006 0.000 ARG F 97 *********************** 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 214 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 TYR cc_start: 0.7068 (m-80) cc_final: 0.6787 (t80) REVERT: A 169 TRP cc_start: 0.8491 (m-10) cc_final: 0.7722 (m-10) REVERT: A 393 LEU cc_start: 0.8140 (tp) cc_final: 0.7905 (tt) REVERT: B 165 VAL cc_start: 0.8332 (t) cc_final: 0.8048 (p) REVERT: B 221 TYR cc_start: 0.5580 (t80) cc_final: 0.5341 (t80) REVERT: B 363 GLN cc_start: 0.7121 (pm20) cc_final: 0.6581 (mp10) REVERT: D 257 ASP cc_start: 0.7590 (p0) cc_final: 0.7132 (p0) REVERT: F 159 LEU cc_start: 0.8813 (tp) cc_final: 0.8525 (tp) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.2578 time to fit residues: 79.6741 Evaluate side-chains 162 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.493 ------------------------------------------------------------------------------- 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: 8.9990 chunk 19 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 147 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- 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 B 348 HIS ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS E 97 ASN F 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.6626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13419 Z= 0.325 Angle : 0.688 7.674 18333 Z= 0.366 Chirality : 0.049 0.189 2116 Planarity : 0.005 0.049 2404 Dihedral : 6.254 79.392 2021 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 0.18 % Allowed : 2.66 % Favored : 97.17 % 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: -1.92 (0.20), residues: 1807 helix: 0.44 (0.22), residues: 635 sheet: -2.24 (0.31), residues: 245 loop : -2.30 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 136 HIS 0.019 0.002 HIS B 327 PHE 0.036 0.002 PHE A 147 TYR 0.024 0.002 TYR C 233 ARG 0.006 0.001 ARG F 71 *********************** 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 203 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 TYR cc_start: 0.7131 (m-80) cc_final: 0.6698 (t80) REVERT: B 165 VAL cc_start: 0.8349 (t) cc_final: 0.8005 (p) REVERT: B 363 GLN cc_start: 0.7346 (pm20) cc_final: 0.6780 (mp10) REVERT: D 257 ASP cc_start: 0.7664 (p0) cc_final: 0.7335 (p0) REVERT: D 280 MET cc_start: 0.7882 (mmm) cc_final: 0.7026 (mmt) outliers start: 2 outliers final: 0 residues processed: 202 average time/residue: 0.2290 time to fit residues: 68.1084 Evaluate side-chains 160 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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: 0.4980 chunk 104 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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** C 286 HIS ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS F 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.6596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13419 Z= 0.206 Angle : 0.591 9.682 18333 Z= 0.310 Chirality : 0.046 0.164 2116 Planarity : 0.004 0.061 2404 Dihedral : 5.643 75.343 2021 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.09 % Allowed : 1.77 % Favored : 98.14 % 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: -1.76 (0.20), residues: 1807 helix: 0.60 (0.22), residues: 646 sheet: -1.98 (0.31), residues: 248 loop : -2.32 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 109 HIS 0.016 0.001 HIS B 327 PHE 0.016 0.001 PHE B 322 TYR 0.019 0.001 TYR D 161 ARG 0.004 0.001 ARG B 210 *********************** 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: 1 poor density : 206 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 TYR cc_start: 0.7031 (m-80) cc_final: 0.6615 (t80) REVERT: A 169 TRP cc_start: 0.8468 (m-10) cc_final: 0.7599 (m-10) REVERT: A 287 PHE cc_start: 0.7437 (m-80) cc_final: 0.7123 (m-80) REVERT: B 165 VAL cc_start: 0.8376 (t) cc_final: 0.8106 (p) REVERT: B 363 GLN cc_start: 0.7252 (pm20) cc_final: 0.6780 (mp10) REVERT: D 257 ASP cc_start: 0.7501 (p0) cc_final: 0.7099 (p0) REVERT: F 159 LEU cc_start: 0.8786 (tp) cc_final: 0.8501 (tp) outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.2466 time to fit residues: 73.7870 Evaluate side-chains 165 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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: 0.7980 chunk 152 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS E 97 ASN F 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.6832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13419 Z= 0.260 Angle : 0.634 9.135 18333 Z= 0.333 Chirality : 0.047 0.163 2116 Planarity : 0.005 0.083 2404 Dihedral : 5.906 78.008 2021 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 0.18 % Allowed : 1.24 % Favored : 98.58 % 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: -1.74 (0.20), residues: 1807 helix: 0.61 (0.22), residues: 633 sheet: -1.98 (0.32), residues: 248 loop : -2.25 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 387 HIS 0.014 0.002 HIS B 327 PHE 0.021 0.002 PHE B 322 TYR 0.016 0.002 TYR F 121 ARG 0.006 0.001 ARG D 287 *********************** 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 203 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 201 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 TYR cc_start: 0.7192 (m-80) cc_final: 0.6618 (t80) REVERT: A 169 TRP cc_start: 0.8465 (m-10) cc_final: 0.7647 (m-10) REVERT: A 202 ILE cc_start: 0.6829 (mp) cc_final: 0.6526 (mt) REVERT: A 316 GLN cc_start: 0.7862 (mp-120) cc_final: 0.7653 (mp10) REVERT: B 71 MET cc_start: 0.3423 (ptt) cc_final: 0.3183 (ptm) REVERT: B 165 VAL cc_start: 0.8348 (t) cc_final: 0.8089 (p) REVERT: B 363 GLN cc_start: 0.7393 (pm20) cc_final: 0.6844 (mp10) REVERT: D 257 ASP cc_start: 0.7608 (p0) cc_final: 0.7266 (p0) REVERT: D 280 MET cc_start: 0.7664 (tpp) cc_final: 0.6319 (mmt) REVERT: F 159 LEU cc_start: 0.8791 (tp) cc_final: 0.8493 (tp) outliers start: 2 outliers final: 0 residues processed: 202 average time/residue: 0.2403 time to fit residues: 70.9206 Evaluate side-chains 153 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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: 0.0270 chunk 81 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 180 optimal weight: 20.0000 chunk 165 optimal weight: 0.6980 chunk 143 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 110 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN F 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13419 Z= 0.145 Angle : 0.568 10.718 18333 Z= 0.289 Chirality : 0.045 0.192 2116 Planarity : 0.004 0.066 2404 Dihedral : 5.224 69.897 2021 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.18 % Allowed : 0.53 % Favored : 99.29 % 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: -1.46 (0.21), residues: 1807 helix: 0.79 (0.22), residues: 647 sheet: -1.94 (0.32), residues: 254 loop : -2.03 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 387 HIS 0.015 0.001 HIS B 327 PHE 0.017 0.001 PHE A 147 TYR 0.020 0.001 TYR D 161 ARG 0.004 0.000 ARG F 158 ********************** 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 209 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 TYR cc_start: 0.6963 (m-80) cc_final: 0.6483 (t80) REVERT: A 169 TRP cc_start: 0.8378 (m-10) cc_final: 0.7651 (m-10) REVERT: A 202 ILE cc_start: 0.6781 (mp) cc_final: 0.6447 (mt) REVERT: A 287 PHE cc_start: 0.7335 (m-80) cc_final: 0.6989 (m-80) REVERT: B 71 MET cc_start: 0.3269 (ptt) cc_final: 0.2982 (ptm) REVERT: B 165 VAL cc_start: 0.8224 (t) cc_final: 0.7933 (p) REVERT: B 336 PHE cc_start: 0.6893 (t80) cc_final: 0.6620 (t80) REVERT: B 363 GLN cc_start: 0.7208 (pm20) cc_final: 0.6701 (mp10) REVERT: D 257 ASP cc_start: 0.7494 (p0) cc_final: 0.7099 (p0) REVERT: D 280 MET cc_start: 0.7584 (tpp) cc_final: 0.7253 (tpt) outliers start: 2 outliers final: 0 residues processed: 208 average time/residue: 0.2518 time to fit residues: 75.8614 Evaluate side-chains 163 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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: 10.0000 chunk 132 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 0.3980 chunk 126 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS F 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.150959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.132076 restraints weight = 27110.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.130603 restraints weight = 35893.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132213 restraints weight = 31336.817| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13419 Z= 0.227 Angle : 0.609 8.213 18333 Z= 0.316 Chirality : 0.046 0.199 2116 Planarity : 0.004 0.047 2404 Dihedral : 5.551 74.411 2021 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.56 % 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: -1.44 (0.21), residues: 1807 helix: 0.82 (0.22), residues: 633 sheet: -1.90 (0.32), residues: 245 loop : -2.01 (0.21), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 387 HIS 0.014 0.001 HIS B 327 PHE 0.018 0.002 PHE B 322 TYR 0.017 0.001 TYR B 188 ARG 0.010 0.001 ARG C 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2651.92 seconds wall clock time: 48 minutes 14.32 seconds (2894.32 seconds total)