Starting phenix.real_space_refine on Thu Nov 16 14:15:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bx7_16311/11_2023/8bx7_16311.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bx7_16311/11_2023/8bx7_16311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bx7_16311/11_2023/8bx7_16311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bx7_16311/11_2023/8bx7_16311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bx7_16311/11_2023/8bx7_16311.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bx7_16311/11_2023/8bx7_16311.pdb" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 10046 2.51 5 N 2644 2.21 5 O 2867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 829": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 838": "OD1" <-> "OD2" Residue "D TYR 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 889": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 894": "OE1" <-> "OE2" Residue "D TYR 946": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 971": "OE1" <-> "OE2" Residue "D PHE 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 995": "OD1" <-> "OD2" Residue "D TYR 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1046": "OD1" <-> "OD2" Residue "D GLU 1108": "OE1" <-> "OE2" Residue "D GLU 1178": "OE1" <-> "OE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 193": "OD1" <-> "OD2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A ASP 457": "OD1" <-> "OD2" Residue "A ASP 480": "OD1" <-> "OD2" Residue "A ASP 538": "OD1" <-> "OD2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 407": "OE1" <-> "OE2" Residue "C TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 538": "OD1" <-> "OD2" Residue "C ASP 570": "OD1" <-> "OD2" Residue "C GLU 581": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 15637 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3561 Classifications: {'peptide': 465} Incomplete info: {'backbone_only': 26, 'truncation_to_alanine': 35} Link IDs: {'PTRANS': 14, 'TRANS': 450} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 125 Chain: "A" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3916 Classifications: {'peptide': 511} Incomplete info: {'backbone_only': 48, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 495} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3954 Classifications: {'peptide': 505} Incomplete info: {'backbone_only': 41, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 490} Chain breaks: 1 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 82 Chain: "C" Number of atoms: 3946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3946 Classifications: {'peptide': 513} Incomplete info: {'backbone_only': 53, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 496} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 103 Chain: "E" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 260 Classifications: {'peptide': 65} Incomplete info: {'backbone_only': 60} Link IDs: {'TRANS': 64} Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 151 Time building chain proxies: 8.39, per 1000 atoms: 0.54 Number of scatterers: 15637 At special positions: 0 Unit cell: (94.86, 122.4, 176.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2867 8.00 N 2644 7.00 C 10046 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: 6.93 Conformation dependent library (CDL) restraints added in 3.2 seconds 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 11 sheets defined 66.0% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'D' and resid 769 through 794 Proline residue: D 789 - end of helix Processing helix chain 'D' and resid 798 through 819 removed outlier: 4.694A pdb=" N HIS D 803 " --> pdb=" O PRO D 799 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU D 804 " --> pdb=" O ASP D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 848 removed outlier: 4.176A pdb=" N VAL D 847 " --> pdb=" O ARG D 843 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS D 848 " --> pdb=" O ASN D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 855 Processing helix chain 'D' and resid 872 through 877 removed outlier: 3.953A pdb=" N ARG D 876 " --> pdb=" O ASN D 872 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 877 " --> pdb=" O PRO D 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 872 through 877' Processing helix chain 'D' and resid 882 through 897 removed outlier: 3.985A pdb=" N PHE D 886 " --> pdb=" O LYS D 882 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 887 " --> pdb=" O TYR D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 931 removed outlier: 3.862A pdb=" N ARG D 904 " --> pdb=" O ALA D 900 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL D 905 " --> pdb=" O TYR D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 957 removed outlier: 3.693A pdb=" N ARG D 948 " --> pdb=" O ASN D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 971 through 1021 removed outlier: 4.225A pdb=" N GLY D 976 " --> pdb=" O ILE D 972 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU D 977 " --> pdb=" O VAL D 973 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLY D1003 " --> pdb=" O ALA D 999 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN D1004 " --> pdb=" O ALA D1000 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1040 Processing helix chain 'D' and resid 1047 through 1053 removed outlier: 4.033A pdb=" N GLN D1053 " --> pdb=" O GLU D1049 " (cutoff:3.500A) Processing helix chain 'D' and resid 1055 through 1067 Processing helix chain 'D' and resid 1067 through 1073 removed outlier: 4.071A pdb=" N VAL D1071 " --> pdb=" O ASN D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1081 through 1091 removed outlier: 4.075A pdb=" N ILE D1085 " --> pdb=" O ASP D1081 " (cutoff:3.500A) Processing helix chain 'D' and resid 1143 through 1149 removed outlier: 3.784A pdb=" N LEU D1148 " --> pdb=" O ILE D1145 " (cutoff:3.500A) Processing helix chain 'D' and resid 1172 through 1182 removed outlier: 4.085A pdb=" N HIS D1182 " --> pdb=" O GLU D1178 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1203 removed outlier: 3.856A pdb=" N LEU D1189 " --> pdb=" O GLU D1185 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN D1201 " --> pdb=" O MET D1197 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN D1202 " --> pdb=" O LEU D1198 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS D1203 " --> pdb=" O ARG D1199 " (cutoff:3.500A) Processing helix chain 'D' and resid 1238 through 1265 Processing helix chain 'A' and resid 160 through 180 removed outlier: 3.722A pdb=" N LEU A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Proline residue: A 173 - end of helix Processing helix chain 'A' and resid 181 through 187 removed outlier: 3.512A pdb=" N PHE A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.850A pdb=" N GLN A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLU A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.950A pdb=" N ILE A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 3.508A pdb=" N ILE A 268 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN A 271 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 288 removed outlier: 3.581A pdb=" N PHE A 282 " --> pdb=" O ARG A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 Processing helix chain 'A' and resid 342 through 360 removed outlier: 3.924A pdb=" N SER A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 402 removed outlier: 3.644A pdb=" N PHE A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 447 through 452 removed outlier: 3.507A pdb=" N LEU A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 576 through 583 Processing helix chain 'A' and resid 586 through 604 Processing helix chain 'A' and resid 619 through 665 Processing helix chain 'B' and resid 160 through 180 Proline residue: B 173 - end of helix Processing helix chain 'B' and resid 181 through 187 Processing helix chain 'B' and resid 194 through 216 removed outlier: 3.616A pdb=" N ASP B 202 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.525A pdb=" N LEU B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 removed outlier: 3.828A pdb=" N ILE B 259 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 274 removed outlier: 3.612A pdb=" N ILE B 268 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASN B 271 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG B 272 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 290 removed outlier: 4.255A pdb=" N MET B 279 " --> pdb=" O ARG B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 324 removed outlier: 3.784A pdb=" N ILE B 323 " --> pdb=" O ILE B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 358 removed outlier: 3.932A pdb=" N SER B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 402 removed outlier: 3.605A pdb=" N PHE B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 422 Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 470 through 474 Processing helix chain 'B' and resid 482 through 492 removed outlier: 3.546A pdb=" N GLU B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 548 removed outlier: 3.894A pdb=" N ILE B 547 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU B 548 " --> pdb=" O GLU B 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 543 through 548' Processing helix chain 'B' and resid 576 through 584 Processing helix chain 'B' and resid 586 through 605 removed outlier: 3.601A pdb=" N GLY B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 664 Processing helix chain 'C' and resid 161 through 187 Proline residue: C 173 - end of helix removed outlier: 5.129A pdb=" N ILE C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 183 " --> pdb=" O THR C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 196 through 218 Processing helix chain 'C' and resid 230 through 239 Processing helix chain 'C' and resid 241 through 252 removed outlier: 3.762A pdb=" N LYS C 245 " --> pdb=" O THR C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.210A pdb=" N ASN C 271 " --> pdb=" O ILE C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 290 removed outlier: 3.582A pdb=" N MET C 279 " --> pdb=" O ARG C 275 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU C 287 " --> pdb=" O PHE C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 324 removed outlier: 3.722A pdb=" N PHE C 296 " --> pdb=" O TYR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'C' and resid 369 through 422 removed outlier: 4.856A pdb=" N ALA C 404 " --> pdb=" O ASN C 400 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ARG C 405 " --> pdb=" O MET C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 442 Processing helix chain 'C' and resid 447 through 454 removed outlier: 3.789A pdb=" N TYR C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 468 Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.508A pdb=" N ALA C 479 " --> pdb=" O ARG C 476 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASP C 480 " --> pdb=" O ILE C 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 476 through 480' Processing helix chain 'C' and resid 482 through 491 Processing helix chain 'C' and resid 576 through 584 Processing helix chain 'C' and resid 586 through 604 removed outlier: 3.964A pdb=" N LYS C 590 " --> pdb=" O TYR C 586 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY C 591 " --> pdb=" O PRO C 587 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 670 removed outlier: 3.523A pdb=" N ARG C 641 " --> pdb=" O THR C 637 " (cutoff:3.500A) Proline residue: C 666 - end of helix Processing helix chain 'E' and resid 86 through 94 Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.957A pdb=" N HIS E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 139 through 148 Processing sheet with id=AA1, first strand: chain 'D' and resid 829 through 831 removed outlier: 3.685A pdb=" N PHE D 829 " --> pdb=" O ILE D 836 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 1093 through 1097 removed outlier: 6.835A pdb=" N ASN D1167 " --> pdb=" O GLN D1117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 1101 through 1104 removed outlier: 6.513A pdb=" N TYR D1102 " --> pdb=" O ALA D1162 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA D1162 " --> pdb=" O TYR D1102 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN D1159 " --> pdb=" O LEU D1124 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL D1121 " --> pdb=" O THR D1135 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR D1135 " --> pdb=" O VAL D1121 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL D1123 " --> pdb=" O LEU D1133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AA5, first strand: chain 'A' and resid 503 through 505 removed outlier: 6.490A pdb=" N TYR A 503 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER A 565 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN A 562 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 534 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AA7, first strand: chain 'B' and resid 532 through 534 removed outlier: 3.832A pdb=" N VAL B 534 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN B 562 " --> pdb=" O VAL B 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 222 through 223 Processing sheet with id=AA9, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AB1, first strand: chain 'C' and resid 503 through 505 removed outlier: 6.128A pdb=" N TYR C 503 " --> pdb=" O SER C 565 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER C 565 " --> pdb=" O TYR C 503 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS C 505 " --> pdb=" O ILE C 563 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 534 " --> pdb=" O VAL C 524 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 100 through 102 1018 hydrogen bonds defined for protein. 2967 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: 5.71 Time building geometry restraints manager: 7.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5070 1.34 - 1.46: 3867 1.46 - 1.58: 6904 1.58 - 1.70: 0 1.70 - 1.82: 134 Bond restraints: 15975 Sorted by residual: bond pdb=" N ILE D1109 " pdb=" CA ILE D1109 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.19e-02 7.06e+03 9.68e+00 bond pdb=" N GLU D1108 " pdb=" CA GLU D1108 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.18e-02 7.18e+03 9.40e+00 bond pdb=" N GLU D1112 " pdb=" CA GLU D1112 " ideal model delta sigma weight residual 1.454 1.492 -0.039 1.34e-02 5.57e+03 8.29e+00 bond pdb=" N ARG D1111 " pdb=" CA ARG D1111 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.21e-02 6.83e+03 5.54e+00 bond pdb=" N ARG D1156 " pdb=" CA ARG D1156 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.25e-02 6.40e+03 5.39e+00 ... (remaining 15970 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.20: 218 105.20 - 112.46: 7696 112.46 - 119.72: 5523 119.72 - 126.99: 7954 126.99 - 134.25: 161 Bond angle restraints: 21552 Sorted by residual: angle pdb=" C LYS B 506 " pdb=" CA LYS B 506 " pdb=" CB LYS B 506 " ideal model delta sigma weight residual 116.63 110.22 6.41 1.16e+00 7.43e-01 3.05e+01 angle pdb=" N GLU D1112 " pdb=" CA GLU D1112 " pdb=" C GLU D1112 " ideal model delta sigma weight residual 110.19 115.77 -5.58 1.24e+00 6.50e-01 2.03e+01 angle pdb=" CB LYS C 453 " pdb=" CG LYS C 453 " pdb=" CD LYS C 453 " ideal model delta sigma weight residual 111.30 121.57 -10.27 2.30e+00 1.89e-01 1.99e+01 angle pdb=" N ILE D 958 " pdb=" CA ILE D 958 " pdb=" C ILE D 958 " ideal model delta sigma weight residual 113.53 109.75 3.78 9.80e-01 1.04e+00 1.49e+01 angle pdb=" N THR C 359 " pdb=" CA THR C 359 " pdb=" C THR C 359 " ideal model delta sigma weight residual 110.35 105.79 4.56 1.38e+00 5.25e-01 1.09e+01 ... (remaining 21547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 7992 17.33 - 34.67: 878 34.67 - 52.00: 202 52.00 - 69.34: 50 69.34 - 86.67: 13 Dihedral angle restraints: 9135 sinusoidal: 3536 harmonic: 5599 Sorted by residual: dihedral pdb=" CA TYR B 568 " pdb=" C TYR B 568 " pdb=" N SER B 569 " pdb=" CA SER B 569 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA ILE C 516 " pdb=" C ILE C 516 " pdb=" N ILE C 517 " pdb=" CA ILE C 517 " ideal model delta harmonic sigma weight residual 180.00 -157.17 -22.83 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA TRP C 198 " pdb=" C TRP C 198 " pdb=" N LEU C 199 " pdb=" CA LEU C 199 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 9132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1507 0.036 - 0.072: 583 0.072 - 0.108: 150 0.108 - 0.144: 31 0.144 - 0.179: 4 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CA MET B 592 " pdb=" N MET B 592 " pdb=" C MET B 592 " pdb=" CB MET B 592 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CA ILE C 517 " pdb=" N ILE C 517 " pdb=" C ILE C 517 " pdb=" CB ILE C 517 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CB ILE B 309 " pdb=" CA ILE B 309 " pdb=" CG1 ILE B 309 " pdb=" CG2 ILE B 309 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 2272 not shown) Planarity restraints: 2780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 773 " 0.022 2.00e-02 2.50e+03 1.97e-02 9.74e+00 pdb=" CG TRP D 773 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP D 773 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 773 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 773 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 773 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 773 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 773 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 773 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 773 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 364 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO A 365 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY D1107 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C GLY D1107 " -0.035 2.00e-02 2.50e+03 pdb=" O GLY D1107 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU D1108 " 0.012 2.00e-02 2.50e+03 ... (remaining 2777 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1749 2.75 - 3.29: 15908 3.29 - 3.82: 26481 3.82 - 4.36: 29402 4.36 - 4.90: 50676 Nonbonded interactions: 124216 Sorted by model distance: nonbonded pdb=" OD2 ASP B 370 " pdb=" NH2 ARG C 342 " model vdw 2.209 2.520 nonbonded pdb=" O PHE B 214 " pdb=" OG1 THR B 217 " model vdw 2.210 2.440 nonbonded pdb=" OD2 ASP C 188 " pdb=" NZ LYS C 321 " model vdw 2.215 2.520 nonbonded pdb=" NH2 ARG D1025 " pdb=" OD1 ASN D1029 " model vdw 2.221 2.520 nonbonded pdb=" OH TYR A 209 " pdb=" O ARG A 272 " model vdw 2.223 2.440 ... (remaining 124211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 154 through 359 or (resid 360 and (name N or name CA or na \ me C or name O or name CB )) or resid 361 through 362 or (resid 363 and (name N \ or name CA or name C or name O or name CB )) or resid 364 through 572 or (resid \ 573 and (name N or name CA or name C or name O or name CB )) or resid 574 throug \ h 601 or (resid 602 through 604 and (name N or name CA or name C or name O or na \ me CB )) or (resid 605 through 613 and (name N or name CA or name C or name O or \ name CB )) or resid 624 through 664)) selection = (chain 'B' and (resid 154 through 215 or (resid 216 and (name N or name CA or na \ me C or name O or name CB or name CG )) or resid 217 through 277 or (resid 278 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 279 \ through 359 or (resid 360 and (name N or name CA or name C or name O or name CB \ )) or resid 361 through 442 or (resid 443 and (name N or name CA or name C or na \ me O or name CB )) or resid 444 through 457 or (resid 458 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 459 through 511 or (resid \ 512 and (name N or name CA or name C or name O or name CB )) or resid 513 throu \ gh 548 or (resid 549 and (name N or name CA or name C or name O or name CB )) or \ resid 550 through 553 or (resid 554 through 555 and (name N or name CA or name \ C or name O or name CB )) or resid 556 through 561 or (resid 562 and (name N or \ name CA or name C or name O or name CB )) or resid 563 through 575 or (resid 576 \ and (name N or name CA or name C or name O or name CB or name CG or name CD )) \ or resid 577 through 601 or (resid 602 through 604 and (name N or name CA or nam \ e C or name O or name CB )) or resid 605 or (resid 606 through 613 and (name N o \ r name CA or name C or name O or name CB )) or resid 624 through 664)) selection = (chain 'C' and (resid 154 through 215 or (resid 216 and (name N or name CA or na \ me C or name O or name CB or name CG )) or resid 217 through 277 or (resid 278 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 279 \ through 362 or (resid 363 and (name N or name CA or name C or name O or name CB \ )) or resid 364 through 442 or (resid 443 and (name N or name CA or name C or na \ me O or name CB )) or resid 444 through 457 or (resid 458 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 459 through 511 or (resid \ 512 and (name N or name CA or name C or name O or name CB )) or resid 513 throu \ gh 548 or (resid 549 and (name N or name CA or name C or name O or name CB )) or \ resid 550 through 561 or (resid 562 and (name N or name CA or name C or name O \ or name CB )) or resid 563 through 572 or (resid 573 and (name N or name CA or n \ ame C or name O or name CB )) or resid 574 through 575 or (resid 576 and (name N \ or name CA or name C or name O or name CB or name CG or name CD )) or resid 577 \ through 603 or (resid 604 and (name N or name CA or name C or name O or name CB \ )) or (resid 605 through 613 and (name N or name CA or name C or name O or name \ CB )) or resid 624 through 664)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.020 Extract box with map and model: 7.670 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 45.050 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 : 0.003 0.062 15975 Z= 0.203 Angle : 0.659 10.266 21552 Z= 0.377 Chirality : 0.040 0.179 2275 Planarity : 0.004 0.060 2780 Dihedral : 15.281 86.671 5695 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.61 % Rotamer: Outliers : 1.92 % Allowed : 19.51 % Favored : 78.57 % 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: 0.66 (0.20), residues: 2039 helix: 1.46 (0.15), residues: 1316 sheet: -0.91 (0.67), residues: 68 loop : -1.54 (0.25), residues: 655 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 181 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 13 residues processed: 203 average time/residue: 1.0989 time to fit residues: 251.6883 Evaluate side-chains 172 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 1.933 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.1680 time to fit residues: 3.3913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 85 optimal weight: 0.0170 chunk 52 optimal weight: 0.9980 chunk 104 optimal weight: 0.0050 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.7234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 891 ASN A 442 ASN B 284 GLN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15975 Z= 0.184 Angle : 0.532 8.267 21552 Z= 0.283 Chirality : 0.040 0.148 2275 Planarity : 0.004 0.055 2780 Dihedral : 3.972 22.548 2254 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.49 % Favored : 94.46 % Rotamer: Outliers : 3.84 % Allowed : 17.53 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.20), residues: 2039 helix: 1.74 (0.15), residues: 1326 sheet: -0.95 (0.65), residues: 68 loop : -1.55 (0.24), residues: 645 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 173 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 21 residues processed: 217 average time/residue: 0.9852 time to fit residues: 244.1273 Evaluate side-chains 179 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 1.783 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 5 average time/residue: 0.7823 time to fit residues: 6.7874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 185 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 165 optimal weight: 0.0370 chunk 184 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 148 optimal weight: 0.7980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1167 ASN B 284 GLN B 417 GLN B 466 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15975 Z= 0.190 Angle : 0.525 9.468 21552 Z= 0.277 Chirality : 0.040 0.163 2275 Planarity : 0.003 0.055 2780 Dihedral : 3.919 22.963 2254 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.44 % Favored : 94.51 % Rotamer: Outliers : 4.03 % Allowed : 18.36 % Favored : 77.61 % 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: 1.13 (0.20), residues: 2039 helix: 1.86 (0.15), residues: 1326 sheet: -0.77 (0.66), residues: 68 loop : -1.48 (0.24), residues: 645 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 172 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 30 residues processed: 217 average time/residue: 0.9671 time to fit residues: 240.2928 Evaluate side-chains 189 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 1.849 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 24 residues processed: 6 average time/residue: 0.6938 time to fit residues: 7.4238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 96 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 197 optimal weight: 9.9990 chunk 97 optimal weight: 0.0670 chunk 176 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN B 494 GLN C 191 GLN C 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15975 Z= 0.197 Angle : 0.528 10.574 21552 Z= 0.276 Chirality : 0.040 0.187 2275 Planarity : 0.003 0.055 2780 Dihedral : 3.873 23.103 2254 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.69 % Favored : 94.26 % Rotamer: Outliers : 4.41 % Allowed : 19.00 % Favored : 76.58 % 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: 1.22 (0.20), residues: 2039 helix: 1.92 (0.15), residues: 1320 sheet: -0.72 (0.65), residues: 68 loop : -1.40 (0.24), residues: 651 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 178 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 31 residues processed: 231 average time/residue: 0.9232 time to fit residues: 245.2193 Evaluate side-chains 189 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 1.962 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 28 residues processed: 3 average time/residue: 0.5206 time to fit residues: 4.5842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 100 optimal weight: 0.5980 chunk 176 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 15975 Z= 0.212 Angle : 0.544 10.875 21552 Z= 0.284 Chirality : 0.041 0.164 2275 Planarity : 0.003 0.055 2780 Dihedral : 3.891 23.471 2254 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.49 % Favored : 94.46 % Rotamer: Outliers : 4.54 % Allowed : 19.77 % Favored : 75.69 % 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: 1.26 (0.20), residues: 2039 helix: 1.93 (0.15), residues: 1320 sheet: -0.21 (0.68), residues: 58 loop : -1.40 (0.24), residues: 661 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 168 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 34 residues processed: 221 average time/residue: 1.0314 time to fit residues: 259.8239 Evaluate side-chains 193 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 159 time to evaluate : 2.016 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 29 residues processed: 5 average time/residue: 0.4858 time to fit residues: 5.6142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 163 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15975 Z= 0.252 Angle : 0.569 9.428 21552 Z= 0.296 Chirality : 0.042 0.155 2275 Planarity : 0.003 0.056 2780 Dihedral : 3.949 24.159 2254 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.31 % Rotamer: Outliers : 4.48 % Allowed : 21.05 % Favored : 74.47 % 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: 1.25 (0.19), residues: 2039 helix: 1.93 (0.15), residues: 1319 sheet: -0.21 (0.68), residues: 58 loop : -1.41 (0.24), residues: 662 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 165 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 41 residues processed: 220 average time/residue: 0.9715 time to fit residues: 245.5836 Evaluate side-chains 199 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 158 time to evaluate : 1.779 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 37 residues processed: 5 average time/residue: 0.4869 time to fit residues: 5.4594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 144 optimal weight: 40.0000 chunk 111 optimal weight: 0.0060 chunk 166 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 196 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN B 417 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15975 Z= 0.203 Angle : 0.559 10.726 21552 Z= 0.290 Chirality : 0.041 0.157 2275 Planarity : 0.003 0.056 2780 Dihedral : 3.911 24.020 2254 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.25 % Favored : 94.70 % Rotamer: Outliers : 4.16 % Allowed : 21.88 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 2039 helix: 2.00 (0.15), residues: 1315 sheet: -0.17 (0.68), residues: 58 loop : -1.36 (0.24), residues: 666 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 173 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 38 residues processed: 226 average time/residue: 0.9985 time to fit residues: 258.4956 Evaluate side-chains 204 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 1.862 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 36 residues processed: 2 average time/residue: 0.8827 time to fit residues: 4.5817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 154 optimal weight: 0.4980 chunk 178 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN B 417 GLN B 494 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15975 Z= 0.177 Angle : 0.551 10.816 21552 Z= 0.285 Chirality : 0.040 0.166 2275 Planarity : 0.003 0.056 2780 Dihedral : 3.841 23.035 2254 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.25 % Favored : 94.70 % Rotamer: Outliers : 3.71 % Allowed : 22.65 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.20), residues: 2039 helix: 2.06 (0.15), residues: 1315 sheet: -0.13 (0.67), residues: 58 loop : -1.33 (0.24), residues: 666 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 176 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 36 residues processed: 224 average time/residue: 0.9745 time to fit residues: 250.8506 Evaluate side-chains 197 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 3.350 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 33 residues processed: 3 average time/residue: 1.3397 time to fit residues: 6.9771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 143 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15975 Z= 0.201 Angle : 0.570 11.267 21552 Z= 0.296 Chirality : 0.041 0.182 2275 Planarity : 0.003 0.056 2780 Dihedral : 3.840 22.907 2254 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.20 % Favored : 94.75 % Rotamer: Outliers : 3.45 % Allowed : 23.22 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.20), residues: 2039 helix: 2.05 (0.15), residues: 1314 sheet: -0.66 (0.64), residues: 68 loop : -1.25 (0.25), residues: 657 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 166 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 36 residues processed: 211 average time/residue: 0.9429 time to fit residues: 229.7173 Evaluate side-chains 197 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 1.887 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 33 residues processed: 4 average time/residue: 0.6617 time to fit residues: 5.7754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 161 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 15975 Z= 0.223 Angle : 0.590 11.195 21552 Z= 0.305 Chirality : 0.042 0.198 2275 Planarity : 0.004 0.071 2780 Dihedral : 3.878 23.133 2254 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.49 % Favored : 94.46 % Rotamer: Outliers : 2.94 % Allowed : 23.80 % Favored : 73.26 % 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: 1.39 (0.20), residues: 2039 helix: 2.03 (0.15), residues: 1314 sheet: -0.53 (0.65), residues: 66 loop : -1.27 (0.25), residues: 659 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 164 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 33 residues processed: 203 average time/residue: 0.9269 time to fit residues: 216.4664 Evaluate side-chains 193 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 1.660 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 33 residues processed: 0 time to fit residues: 2.3311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 162 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.137245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.102936 restraints weight = 27502.365| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.77 r_work: 0.3463 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15975 Z= 0.236 Angle : 0.604 11.300 21552 Z= 0.312 Chirality : 0.042 0.215 2275 Planarity : 0.004 0.073 2780 Dihedral : 3.919 23.414 2254 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.69 % Favored : 94.26 % Rotamer: Outliers : 3.07 % Allowed : 23.54 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 2039 helix: 2.01 (0.15), residues: 1314 sheet: -0.51 (0.66), residues: 66 loop : -1.26 (0.25), residues: 659 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5016.09 seconds wall clock time: 90 minutes 27.60 seconds (5427.60 seconds total)