Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 22:50:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d33_27154/07_2023/8d33_27154_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d33_27154/07_2023/8d33_27154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d33_27154/07_2023/8d33_27154.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d33_27154/07_2023/8d33_27154.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d33_27154/07_2023/8d33_27154_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d33_27154/07_2023/8d33_27154_updated.pdb" } resolution = 2.46 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= 0.325 sd= 0.631 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 Ca 1 9.91 5 P 49 5.49 5 S 82 5.16 5 C 9585 2.51 5 N 2683 2.21 5 O 2872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 15272 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7778 Classifications: {'peptide': 974} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 65, 'TRANS': 908} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3307 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3213 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "T" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 494 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' CA': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.57, per 1000 atoms: 0.50 Number of scatterers: 15272 At special positions: 0 Unit cell: (107.1, 124.95, 153, 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) Ca 1 19.99 S 82 16.00 P 49 15.00 O 2872 8.00 N 2683 7.00 C 9585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A1077 " distance=2.04 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: 6.40 Conformation dependent library (CDL) restraints added in 2.3 seconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3322 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 10 sheets defined 42.2% alpha, 13.2% beta 22 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 5.56 Creating SS restraints... Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 135 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 226 through 229 No H-bonds generated for 'chain 'A' and resid 226 through 229' Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.873A pdb=" N HIS A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 376 through 379 No H-bonds generated for 'chain 'A' and resid 376 through 379' Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 389 through 417 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 421 through 431 removed outlier: 3.659A pdb=" N GLY A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 481 removed outlier: 3.523A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N SER A 475 " --> pdb=" O CYS A 471 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N TYR A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU A 481 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 571 through 576 removed outlier: 3.677A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 649 through 660 Processing helix chain 'A' and resid 768 through 776 Proline residue: A 772 - end of helix removed outlier: 3.502A pdb=" N ASP A 776 " --> pdb=" O LYS A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 809 removed outlier: 5.079A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 823 through 826 No H-bonds generated for 'chain 'A' and resid 823 through 826' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 915 through 922 removed outlier: 3.712A pdb=" N GLN A 922 " --> pdb=" O TRP A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 939 Processing helix chain 'A' and resid 943 through 954 Processing helix chain 'A' and resid 959 through 969 Processing helix chain 'A' and resid 975 through 986 removed outlier: 3.750A pdb=" N MET A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1066 Processing helix chain 'A' and resid 1081 through 1083 No H-bonds generated for 'chain 'A' and resid 1081 through 1083' Processing helix chain 'A' and resid 1093 through 1122 removed outlier: 3.572A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1168 removed outlier: 4.807A pdb=" N TYR A1147 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A1149 " --> pdb=" O ARG A1146 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A1159 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET A1163 " --> pdb=" O THR A1160 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS A1167 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1206 through 1209 No H-bonds generated for 'chain 'A' and resid 1206 through 1209' Processing helix chain 'A' and resid 1220 through 1227 Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 101 through 118 Processing helix chain 'B' and resid 151 through 153 No H-bonds generated for 'chain 'B' and resid 151 through 153' Processing helix chain 'B' and resid 166 through 177 removed outlier: 4.234A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.620A pdb=" N HIS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 245 through 265 removed outlier: 5.160A pdb=" N ASN B 249 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TRP B 255 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG B 259 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP B 263 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 319 through 322 Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.638A pdb=" N PHE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 392 through 409 removed outlier: 3.657A pdb=" N ASN B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 425 through 435 Processing helix chain 'B' and resid 445 through 450 Processing helix chain 'B' and resid 468 through 484 removed outlier: 4.492A pdb=" N LYS B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ASP B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASN B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 101 through 118 Processing helix chain 'C' and resid 151 through 157 removed outlier: 5.274A pdb=" N ILE C 156 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 177 removed outlier: 3.638A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 196 removed outlier: 3.730A pdb=" N HIS C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 265 removed outlier: 3.538A pdb=" N SER C 248 " --> pdb=" O PRO C 245 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASN C 249 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 342 through 353 Processing helix chain 'C' and resid 392 through 409 Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 425 through 434 Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.835A pdb=" N GLU C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 450 " --> pdb=" O THR C 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 445 through 450' Processing helix chain 'C' and resid 468 through 484 removed outlier: 4.610A pdb=" N LYS C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.910A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA A 212 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA A 214 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 196 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N SER A 216 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N ALA A 194 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU A 265 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE A 197 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 267 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N VAL A 199 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG A 290 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLY A 268 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 292 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 435 through 438 Processing sheet with id= C, first strand: chain 'A' and resid 612 through 615 Processing sheet with id= D, first strand: chain 'A' and resid 1216 through 1218 removed outlier: 5.505A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.800A pdb=" N GLY B 207 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY B 307 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N SER B 337 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASN B 305 " --> pdb=" O SER B 337 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASN B 339 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU B 303 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP B 341 " --> pdb=" O GLU B 301 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU B 301 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 289 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR B 302 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN B 287 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N TRP B 304 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LYS B 285 " --> pdb=" O TRP B 304 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 324 through 326 Processing sheet with id= G, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.079A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE B 439 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ASP B 386 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 441 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.789A pdb=" N GLY C 207 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU C 289 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N THR C 302 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN C 287 " --> pdb=" O THR C 302 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 323 through 326 Processing sheet with id= J, first strand: chain 'C' and resid 413 through 415 removed outlier: 7.244A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N PHE C 439 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ASP C 386 " --> pdb=" O PHE C 439 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 441 " --> pdb=" O ASP C 386 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 6.15 Time building geometry restraints manager: 6.53 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: 4795 1.34 - 1.46: 3021 1.46 - 1.58: 7714 1.58 - 1.70: 91 1.70 - 1.82: 130 Bond restraints: 15751 Sorted by residual: bond pdb=" O5' DCP A1302 " pdb=" PA DCP A1302 " ideal model delta sigma weight residual 1.579 1.805 -0.226 1.50e-02 4.44e+03 2.28e+02 bond pdb=" C5' DCP A1302 " pdb=" O5' DCP A1302 " ideal model delta sigma weight residual 1.443 1.323 0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" O3A DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 1.592 1.707 -0.115 1.10e-02 8.26e+03 1.09e+02 bond pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 1.600 1.650 -0.050 1.10e-02 8.26e+03 2.10e+01 bond pdb=" C4 DCP A1302 " pdb=" N4 DCP A1302 " ideal model delta sigma weight residual 1.334 1.389 -0.055 1.20e-02 6.94e+03 2.06e+01 ... (remaining 15746 not shown) Histogram of bond angle deviations from ideal: 92.69 - 101.18: 42 101.18 - 109.68: 2286 109.68 - 118.18: 9923 118.18 - 126.67: 8805 126.67 - 135.17: 491 Bond angle restraints: 21547 Sorted by residual: angle pdb=" O2B DCP A1302 " pdb=" PB DCP A1302 " pdb=" O3B DCP A1302 " ideal model delta sigma weight residual 106.94 123.84 -16.90 1.88e+00 2.83e-01 8.08e+01 angle pdb=" O2A DCP A1302 " pdb=" PA DCP A1302 " pdb=" O3A DCP A1302 " ideal model delta sigma weight residual 106.94 123.75 -16.81 1.88e+00 2.83e-01 8.00e+01 angle pdb=" PB DCP A1302 " pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 139.87 132.92 6.95 1.00e+00 1.00e+00 4.83e+01 angle pdb=" O2G DCP A1302 " pdb=" PG DCP A1302 " pdb=" O3B DCP A1302 " ideal model delta sigma weight residual 104.48 97.94 6.54 1.14e+00 7.76e-01 3.32e+01 angle pdb=" C1' DCP A1302 " pdb=" N1 DCP A1302 " pdb=" C6 DCP A1302 " ideal model delta sigma weight residual 121.66 114.58 7.08 1.39e+00 5.21e-01 2.61e+01 ... (remaining 21542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8582 17.84 - 35.68: 455 35.68 - 53.52: 140 53.52 - 71.36: 35 71.36 - 89.20: 12 Dihedral angle restraints: 9224 sinusoidal: 4077 harmonic: 5147 Sorted by residual: dihedral pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " pdb=" SG CYS A1077 " pdb=" CB CYS A1077 " ideal model delta sinusoidal sigma weight residual 93.00 130.66 -37.66 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CA LEU A 195 " pdb=" C LEU A 195 " pdb=" N VAL A 196 " pdb=" CA VAL A 196 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLU A 181 " pdb=" C GLU A 181 " pdb=" N GLY A 182 " pdb=" CA GLY A 182 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 9221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1558 0.030 - 0.060: 505 0.060 - 0.089: 141 0.089 - 0.119: 97 0.119 - 0.149: 21 Chirality restraints: 2322 Sorted by residual: chirality pdb=" C4' DCP A1302 " pdb=" C3' DCP A1302 " pdb=" C5' DCP A1302 " pdb=" O4' DCP A1302 " both_signs ideal model delta sigma weight residual False -2.50 -2.65 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA ILE A 744 " pdb=" N ILE A 744 " pdb=" C ILE A 744 " pdb=" CB ILE A 744 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA VAL B 332 " pdb=" N VAL B 332 " pdb=" C VAL B 332 " pdb=" CB VAL B 332 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 2319 not shown) Planarity restraints: 2602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 452 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.55e+00 pdb=" C TYR A 452 " 0.022 2.00e-02 2.50e+03 pdb=" O TYR A 452 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU A 453 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC T 21 " -0.015 2.00e-02 2.50e+03 7.52e-03 1.27e+00 pdb=" N1 DC T 21 " 0.016 2.00e-02 2.50e+03 pdb=" C2 DC T 21 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC T 21 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DC T 21 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DC T 21 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC T 21 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC T 21 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC T 21 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 482 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.18e+00 pdb=" N PRO A 483 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 483 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 483 " 0.015 5.00e-02 4.00e+02 ... (remaining 2599 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 206 2.65 - 3.21: 13937 3.21 - 3.78: 23250 3.78 - 4.34: 33045 4.34 - 4.90: 52166 Nonbonded interactions: 122604 Sorted by model distance: nonbonded pdb=" OE2 GLU B 165 " pdb=" NZ LYS C 160 " model vdw 2.091 2.520 nonbonded pdb=" O THR B 460 " pdb=" OG1 THR B 461 " model vdw 2.095 2.440 nonbonded pdb=" OG SER A1230 " pdb=" OE1 GLU A1232 " model vdw 2.105 2.440 nonbonded pdb=" O PRO A 217 " pdb=" OG SER A 218 " model vdw 2.125 2.440 nonbonded pdb=" O THR C 460 " pdb=" OG1 THR C 461 " model vdw 2.130 2.440 ... (remaining 122599 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 'B' and (resid 67 through 218 or (resid 219 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 228 and (name N or name CA or name C or na \ me O or name CB )) or resid 229 through 355 or resid 368 through 485)) selection = chain 'C' } 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: 1.430 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: 8.390 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 44.400 Find NCS groups from input model: 0.640 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:15.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 0.226 15751 Z= 0.183 Angle : 0.546 16.903 21547 Z= 0.306 Chirality : 0.038 0.149 2322 Planarity : 0.003 0.027 2602 Dihedral : 13.003 89.196 5899 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer Outliers : 0.39 % 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: 0.90 (0.21), residues: 1758 helix: 1.34 (0.20), residues: 739 sheet: 0.94 (0.31), residues: 242 loop : -0.16 (0.23), residues: 777 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 488 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 492 average time/residue: 1.3518 time to fit residues: 728.4564 Evaluate side-chains 385 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 384 time to evaluate : 1.665 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2952 time to fit residues: 2.6984 ------------------------------------------------------------------------------- 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: 2.9990 chunk 137 optimal weight: 0.0970 chunk 76 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 chunk 164 optimal weight: 9.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 110 HIS A 115 GLN A 264 GLN A 398 GLN A 564 GLN A 736 ASN A 843 GLN A1059 ASN A1098 ASN A1157 ASN A1175 GLN B 195 ASN B 339 ASN B 409 ASN C 258 HIS C 339 ASN C 400 GLN C 409 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 15751 Z= 0.156 Angle : 0.547 8.188 21547 Z= 0.285 Chirality : 0.040 0.139 2322 Planarity : 0.004 0.038 2602 Dihedral : 13.344 60.561 2390 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.56 % Favored : 97.38 % Rotamer Outliers : 2.65 % 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: 1.23 (0.21), residues: 1758 helix: 1.56 (0.20), residues: 743 sheet: 1.23 (0.31), residues: 243 loop : 0.02 (0.24), residues: 772 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 389 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 8 residues processed: 404 average time/residue: 1.2576 time to fit residues: 560.3610 Evaluate side-chains 373 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 365 time to evaluate : 1.815 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 1.3352 time to fit residues: 6.8279 ------------------------------------------------------------------------------- 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: 9.9990 chunk 51 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 45 optimal weight: 0.1980 chunk 164 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 264 GLN A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1059 ASN A1175 GLN B 195 ASN B 323 HIS ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN C 339 ASN C 400 GLN C 409 ASN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.134 15751 Z= 0.522 Angle : 0.816 12.113 21547 Z= 0.432 Chirality : 0.053 0.238 2322 Planarity : 0.008 0.077 2602 Dihedral : 14.088 65.803 2390 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.66 % Favored : 95.28 % Rotamer Outliers : 4.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.19), residues: 1758 helix: 0.45 (0.19), residues: 747 sheet: 0.88 (0.32), residues: 232 loop : -0.62 (0.22), residues: 779 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 352 time to evaluate : 1.770 Fit side-chains revert: symmetry clash outliers start: 77 outliers final: 43 residues processed: 394 average time/residue: 1.2957 time to fit residues: 561.0846 Evaluate side-chains 377 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 334 time to evaluate : 1.644 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 28 residues processed: 15 average time/residue: 0.8728 time to fit residues: 17.2167 ------------------------------------------------------------------------------- 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: 6.9990 chunk 123 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 308 GLN A 564 GLN A 736 ASN A 843 GLN A1059 ASN A1157 ASN A1175 GLN B 195 ASN B 339 ASN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.085 15751 Z= 0.304 Angle : 0.666 8.547 21547 Z= 0.353 Chirality : 0.045 0.155 2322 Planarity : 0.006 0.055 2602 Dihedral : 13.994 64.482 2390 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer Outliers : 5.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 1758 helix: 0.55 (0.19), residues: 747 sheet: 0.93 (0.32), residues: 227 loop : -0.58 (0.22), residues: 784 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 355 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 45 residues processed: 406 average time/residue: 1.3671 time to fit residues: 611.3230 Evaluate side-chains 390 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 345 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 32 residues processed: 13 average time/residue: 0.7154 time to fit residues: 13.1986 ------------------------------------------------------------------------------- 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: 5.9990 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 277 HIS A 564 GLN A 736 ASN A 843 GLN A1059 ASN A1175 GLN B 195 ASN B 339 ASN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.118 15751 Z= 0.443 Angle : 0.779 11.630 21547 Z= 0.410 Chirality : 0.050 0.211 2322 Planarity : 0.007 0.068 2602 Dihedral : 14.209 65.338 2390 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.95 % Favored : 94.99 % Rotamer Outliers : 5.88 % 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: -0.31 (0.19), residues: 1758 helix: 0.22 (0.19), residues: 746 sheet: 0.66 (0.31), residues: 242 loop : -0.83 (0.22), residues: 770 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 340 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 59 residues processed: 402 average time/residue: 1.3335 time to fit residues: 588.6892 Evaluate side-chains 388 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 329 time to evaluate : 1.630 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 41 residues processed: 18 average time/residue: 0.6141 time to fit residues: 15.5631 ------------------------------------------------------------------------------- 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: 2.9990 chunk 157 optimal weight: 0.0670 chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 0.1980 overall best weight: 1.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1059 ASN A1157 ASN A1175 GLN B 187 HIS B 195 ASN ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN C 422 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 15751 Z= 0.229 Angle : 0.627 9.421 21547 Z= 0.331 Chirality : 0.043 0.148 2322 Planarity : 0.005 0.048 2602 Dihedral : 14.045 63.646 2390 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.36 % Rotamer Outliers : 5.36 % 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: 0.12 (0.20), residues: 1758 helix: 0.60 (0.19), residues: 748 sheet: 0.90 (0.31), residues: 236 loop : -0.62 (0.22), residues: 774 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 359 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 51 residues processed: 419 average time/residue: 1.3059 time to fit residues: 601.9718 Evaluate side-chains 391 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 340 time to evaluate : 1.690 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 42 residues processed: 9 average time/residue: 0.6004 time to fit residues: 8.6354 ------------------------------------------------------------------------------- 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: 9.9990 chunk 19 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 147 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 109 optimal weight: 0.1980 chunk 106 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 564 GLN A 659 HIS A 736 ASN A 843 GLN A1059 ASN A1175 GLN B 195 ASN B 339 ASN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN C 409 ASN C 422 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 15751 Z= 0.161 Angle : 0.571 10.075 21547 Z= 0.296 Chirality : 0.040 0.146 2322 Planarity : 0.005 0.079 2602 Dihedral : 13.943 60.848 2390 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.76 % Rotamer Outliers : 4.52 % 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: 0.54 (0.20), residues: 1758 helix: 0.95 (0.19), residues: 751 sheet: 1.16 (0.32), residues: 243 loop : -0.43 (0.23), residues: 764 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 370 time to evaluate : 1.812 Fit side-chains revert: symmetry clash outliers start: 70 outliers final: 51 residues processed: 422 average time/residue: 1.2398 time to fit residues: 579.4264 Evaluate side-chains 401 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 350 time to evaluate : 1.703 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 40 residues processed: 11 average time/residue: 0.4775 time to fit residues: 8.9872 ------------------------------------------------------------------------------- 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: 4.9990 chunk 104 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 137 optimal weight: 0.0970 chunk 158 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 468 ASN A 564 GLN A 659 HIS A 736 ASN A 843 GLN A1157 ASN A1175 GLN B 195 ASN B 258 HIS ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN C 339 ASN C 400 GLN C 409 ASN C 422 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 15751 Z= 0.151 Angle : 0.563 10.793 21547 Z= 0.290 Chirality : 0.039 0.153 2322 Planarity : 0.004 0.043 2602 Dihedral : 13.913 60.239 2390 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.81 % Rotamer Outliers : 4.13 % 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: 0.75 (0.20), residues: 1758 helix: 1.13 (0.20), residues: 749 sheet: 1.36 (0.32), residues: 236 loop : -0.34 (0.22), residues: 773 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 363 time to evaluate : 1.695 Fit side-chains revert: symmetry clash outliers start: 64 outliers final: 43 residues processed: 412 average time/residue: 1.2024 time to fit residues: 549.7812 Evaluate side-chains 392 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 349 time to evaluate : 1.755 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 37 residues processed: 6 average time/residue: 0.9332 time to fit residues: 8.6997 ------------------------------------------------------------------------------- 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: 6.9990 chunk 152 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 153 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 171 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN A 270 ASN A 468 ASN A 564 GLN A 659 HIS A 736 ASN A 843 GLN A1059 ASN A1157 ASN A1175 GLN B 195 ASN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 GLN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN C 409 ASN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.121 15751 Z= 0.448 Angle : 0.779 11.074 21547 Z= 0.406 Chirality : 0.050 0.194 2322 Planarity : 0.007 0.063 2602 Dihedral : 14.101 64.512 2390 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.38 % Favored : 95.56 % Rotamer Outliers : 4.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1758 helix: 0.47 (0.19), residues: 748 sheet: 0.92 (0.31), residues: 243 loop : -0.62 (0.22), residues: 767 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 347 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 45 residues processed: 393 average time/residue: 1.2473 time to fit residues: 541.1664 Evaluate side-chains 388 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 343 time to evaluate : 1.768 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 39 residues processed: 6 average time/residue: 0.7799 time to fit residues: 7.8604 ------------------------------------------------------------------------------- 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: 0.8980 chunk 81 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 308 GLN A 564 GLN A 659 HIS A 736 ASN A 843 GLN A1059 ASN A1157 ASN A1175 GLN B 195 ASN ** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN B 339 ASN B 355 GLN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 15751 Z= 0.227 Angle : 0.640 10.451 21547 Z= 0.333 Chirality : 0.043 0.162 2322 Planarity : 0.005 0.047 2602 Dihedral : 14.002 62.689 2390 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.36 % Rotamer Outliers : 3.75 % 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: 0.31 (0.20), residues: 1758 helix: 0.73 (0.19), residues: 751 sheet: 1.13 (0.32), residues: 236 loop : -0.53 (0.23), residues: 771 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 353 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 47 residues processed: 397 average time/residue: 1.2698 time to fit residues: 557.9568 Evaluate side-chains 388 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 341 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 40 residues processed: 7 average time/residue: 0.7835 time to fit residues: 8.7044 ------------------------------------------------------------------------------- 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: 3.9990 chunk 132 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 126 optimal weight: 0.0050 chunk 8 optimal weight: 3.9990 overall best weight: 1.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 270 ASN A 564 GLN A 659 HIS A 736 ASN A 843 GLN A1059 ASN A1175 GLN B 195 ASN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 355 GLN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN C 409 ASN ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.123232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.115074 restraints weight = 26144.995| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.39 r_work: 0.3571 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 15751 Z= 0.221 Angle : 0.637 10.190 21547 Z= 0.331 Chirality : 0.042 0.164 2322 Planarity : 0.005 0.045 2602 Dihedral : 13.971 62.199 2390 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.04 % Favored : 95.90 % Rotamer Outliers : 3.62 % 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: 0.37 (0.20), residues: 1758 helix: 0.80 (0.19), residues: 752 sheet: 1.05 (0.31), residues: 243 loop : -0.50 (0.23), residues: 763 =============================================================================== Job complete usr+sys time: 8115.43 seconds wall clock time: 143 minutes 21.45 seconds (8601.45 seconds total)