Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 22:34:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w18_21503/07_2023/6w18_21503_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w18_21503/07_2023/6w18_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_21503/07_2023/6w18_21503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w18_21503/07_2023/6w18_21503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w18_21503/07_2023/6w18_21503_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w18_21503/07_2023/6w18_21503_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 6.36, per 1000 atoms: 0.48 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: 4.90 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... 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: 1.10 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: 3.67 Time building geometry restraints manager: 5.35 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: 7431 17.45 - 34.90: 366 34.90 - 52.35: 68 52.35 - 69.81: 7 69.81 - 87.26: 6 Dihedral angle restraints: 7878 sinusoidal: 2531 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 7875 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: 0.010 Normalize map: mean=0, sd=1: 0.850 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: 4.460 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 33.550 Find NCS groups from input model: 0.430 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.260 ------------------------------------------------------------------------------- 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 : 11.010 87.256 4414 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 % 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 *********************** 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 : 1.442 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 outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.2747 time to fit residues: 143.9124 Evaluate side-chains 200 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.489 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0486 ------------------------------------------------------------------------------- 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: 0.8980 chunk 46 optimal weight: 0.0070 chunk 92 optimal weight: 0.6980 chunk 73 optimal weight: 0.0770 chunk 141 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 HIS A 404 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.2492 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= 0.132 Angle : 0.483 5.584 18333 Z= 0.245 Chirality : 0.043 0.183 2116 Planarity : 0.003 0.043 2404 Dihedral : 3.170 66.700 1959 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.19), residues: 1807 helix: 0.60 (0.21), residues: 628 sheet: -2.81 (0.29), residues: 226 loop : -2.73 (0.18), residues: 953 *********************** 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 269 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 269 average time/residue: 0.2416 time to fit residues: 94.8731 Evaluate side-chains 189 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 1.390 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1109 time to fit residues: 2.4280 ------------------------------------------------------------------------------- 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: 0.7980 chunk 51 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 164 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 163 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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** A 138 ASN ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 GLN ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.074 13419 Z= 0.402 Angle : 0.767 10.399 18333 Z= 0.409 Chirality : 0.052 0.230 2116 Planarity : 0.006 0.067 2404 Dihedral : 5.326 69.006 1959 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.41 % Favored : 91.53 % Rotamer Outliers : 0.35 % 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: -2.67 (0.19), residues: 1807 helix: -0.14 (0.20), residues: 663 sheet: -2.65 (0.30), residues: 253 loop : -2.86 (0.19), residues: 891 *********************** 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 : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 219 average time/residue: 0.2547 time to fit residues: 81.5690 Evaluate side-chains 151 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 time to evaluate : 1.457 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1284 time to fit residues: 2.5228 ------------------------------------------------------------------------------- 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: 1.9990 chunk 85 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 0.0670 chunk 110 optimal weight: 7.9990 chunk 165 optimal weight: 0.8980 chunk 174 optimal weight: 20.0000 chunk 86 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 chunk 47 optimal weight: 30.0000 overall best weight: 0.8920 ------------------------------------------------------------------------------- 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** A 379 HIS B 265 HIS C 8 HIS D 160 HIS ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 13419 Z= 0.145 Angle : 0.532 7.590 18333 Z= 0.272 Chirality : 0.044 0.165 2116 Planarity : 0.004 0.046 2404 Dihedral : 4.193 73.159 1959 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.20), residues: 1807 helix: 0.63 (0.21), residues: 644 sheet: -2.26 (0.32), residues: 242 loop : -2.47 (0.20), residues: 921 *********************** 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 220 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 219 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 220 average time/residue: 0.2607 time to fit residues: 82.5373 Evaluate side-chains 160 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.475 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1308 time to fit residues: 2.2443 ------------------------------------------------------------------------------- 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: 9.9990 chunk 99 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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** A 151 ASN ** A 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS D 173 HIS E 97 ASN F 60 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.6554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.081 13419 Z= 0.447 Angle : 0.783 9.542 18333 Z= 0.421 Chirality : 0.052 0.261 2116 Planarity : 0.006 0.053 2404 Dihedral : 5.924 79.941 1959 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer Outliers : 0.44 % 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: -2.56 (0.19), residues: 1807 helix: -0.14 (0.20), residues: 658 sheet: -2.35 (0.32), residues: 231 loop : -2.79 (0.20), residues: 918 *********************** 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 200 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 195 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 199 average time/residue: 0.2495 time to fit residues: 72.6875 Evaluate side-chains 154 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.442 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9779 ------------------------------------------------------------------------------- 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: 5.9990 chunk 157 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 102 optimal weight: 0.0570 chunk 43 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.5102 ------------------------------------------------------------------------------- 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 379 HIS ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN D 160 HIS F 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.6393 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= 0.192 Angle : 0.590 9.380 18333 Z= 0.308 Chirality : 0.045 0.186 2116 Planarity : 0.004 0.046 2404 Dihedral : 4.909 87.472 1959 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.20), residues: 1807 helix: 0.48 (0.22), residues: 632 sheet: -2.29 (0.29), residues: 278 loop : -2.42 (0.21), residues: 897 *********************** 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 224 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.2386 time to fit residues: 78.0274 Evaluate side-chains 159 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.542 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9164 ------------------------------------------------------------------------------- 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: 0.6980 chunk 19 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 147 optimal weight: 30.0000 chunk 97 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 109 optimal weight: 0.3980 chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 379 HIS ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7040 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13419 Z= 0.183 Angle : 0.577 10.036 18333 Z= 0.299 Chirality : 0.045 0.160 2116 Planarity : 0.004 0.045 2404 Dihedral : 4.661 85.283 1959 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer Outliers : 0.18 % 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: -1.83 (0.20), residues: 1807 helix: 0.65 (0.22), residues: 639 sheet: -2.26 (0.30), residues: 267 loop : -2.33 (0.21), residues: 901 *********************** 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 217 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 215 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 216 average time/residue: 0.2510 time to fit residues: 79.2932 Evaluate side-chains 160 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9658 ------------------------------------------------------------------------------- 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: 7.9990 chunk 104 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 137 optimal weight: 40.0000 chunk 158 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 379 HIS 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: 0.7195 moved from start: 0.6991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 13419 Z= 0.334 Angle : 0.708 11.440 18333 Z= 0.375 Chirality : 0.049 0.176 2116 Planarity : 0.005 0.094 2404 Dihedral : 5.474 85.510 1959 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer Outliers : 0.18 % 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: -2.14 (0.20), residues: 1807 helix: 0.34 (0.22), residues: 643 sheet: -2.37 (0.30), residues: 260 loop : -2.51 (0.20), residues: 904 *********************** 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 204 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 203 average time/residue: 0.2447 time to fit residues: 73.4942 Evaluate side-chains 154 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.551 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0840 ------------------------------------------------------------------------------- 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: 0.9980 chunk 152 optimal weight: 4.9990 chunk 162 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 171 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 HIS C 286 HIS D 160 HIS ** 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: 0.6994 moved from start: 0.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 13419 Z= 0.147 Angle : 0.575 10.373 18333 Z= 0.293 Chirality : 0.044 0.163 2116 Planarity : 0.004 0.048 2404 Dihedral : 4.576 87.734 1959 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.21), residues: 1807 helix: 0.75 (0.22), residues: 633 sheet: -2.20 (0.29), residues: 279 loop : -2.13 (0.21), residues: 895 *********************** 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 215 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.2572 time to fit residues: 80.1894 Evaluate side-chains 156 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0113 ------------------------------------------------------------------------------- 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: 0.0870 chunk 81 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 114 optimal weight: 0.4980 chunk 152 optimal weight: 5.9990 overall best weight: 3.7164 ------------------------------------------------------------------------------- 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 379 HIS ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7207 moved from start: 0.7251 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= 0.354 Angle : 0.719 10.735 18333 Z= 0.381 Chirality : 0.049 0.171 2116 Planarity : 0.005 0.051 2404 Dihedral : 5.468 88.460 1959 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer Outliers : 0.18 % 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: -2.08 (0.20), residues: 1807 helix: 0.35 (0.22), residues: 634 sheet: -2.37 (0.29), residues: 270 loop : -2.39 (0.20), residues: 903 ********************** 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 196 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 194 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 195 average time/residue: 0.2517 time to fit residues: 72.7072 Evaluate side-chains 153 residues out of total 1601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.450 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9747 ------------------------------------------------------------------------------- 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: 6.9990 chunk 132 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 147 optimal weight: 0.0670 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 126 optimal weight: 0.0030 chunk 8 optimal weight: 0.7980 overall best weight: 1.1530 ------------------------------------------------------------------------------- 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 379 HIS D 160 HIS D 173 HIS F 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.152512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.133163 restraints weight = 26927.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132539 restraints weight = 37331.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.133862 restraints weight = 30528.938| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13419 Z= 0.170 Angle : 0.590 9.478 18333 Z= 0.302 Chirality : 0.045 0.160 2116 Planarity : 0.004 0.048 2404 Dihedral : 4.736 85.990 1959 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer Outliers : 0.18 % 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: -1.63 (0.21), residues: 1807 helix: 0.76 (0.22), residues: 628 sheet: -2.14 (0.30), residues: 266 loop : -2.13 (0.21), residues: 913 =============================================================================== Job complete usr+sys time: 2473.04 seconds wall clock time: 45 minutes 39.88 seconds (2739.88 seconds total)