Starting phenix.real_space_refine on Sun Dec 10 18:54:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d33_27154/12_2023/8d33_27154_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d33_27154/12_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_27154/12_2023/8d33_27154.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d33_27154/12_2023/8d33_27154.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d33_27154/12_2023/8d33_27154_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d33_27154/12_2023/8d33_27154_updated.pdb" } resolution = 2.46 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= 0.325 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-1.21rc1-5172/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: 8.07, per 1000 atoms: 0.53 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: 6.64 Conformation dependent library (CDL) restraints added in 2.8 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: 6.79 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: 5.46 Time building geometry restraints manager: 7.07 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: 8613 17.84 - 35.68: 483 35.68 - 53.52: 148 53.52 - 71.36: 35 71.36 - 89.20: 13 Dihedral angle restraints: 9292 sinusoidal: 4145 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 9289 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.850 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 47.350 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.490 ------------------------------------------------------------------------------- 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 : 13.188 89.196 5967 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 % Allowed : 4.39 % Favored : 95.22 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 220 HIS 0.002 0.001 HIS C 187 PHE 0.014 0.001 PHE A 197 TYR 0.009 0.001 TYR A1108 ARG 0.003 0.000 ARG A 574 *********************** 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 : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 492 average time/residue: 1.3179 time to fit residues: 711.7218 Evaluate side-chains 385 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 384 time to evaluate : 1.691 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3417 time to fit residues: 2.8549 ------------------------------------------------------------------------------- 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 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15751 Z= 0.156 Angle : 0.543 7.355 21547 Z= 0.284 Chirality : 0.040 0.140 2322 Planarity : 0.004 0.034 2602 Dihedral : 13.728 76.441 2458 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Rotamer: Outliers : 2.52 % Allowed : 15.83 % Favored : 81.65 % 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: 1.24 (0.21), residues: 1758 helix: 1.57 (0.20), residues: 743 sheet: 1.23 (0.31), residues: 243 loop : 0.03 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 175 HIS 0.003 0.001 HIS C 77 PHE 0.022 0.001 PHE A 197 TYR 0.018 0.001 TYR C 206 ARG 0.008 0.000 ARG A 657 *********************** 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 428 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 389 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 8 residues processed: 402 average time/residue: 1.2461 time to fit residues: 553.0139 Evaluate side-chains 373 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 365 time to evaluate : 1.785 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 4 residues processed: 4 average time/residue: 0.9827 time to fit residues: 6.6844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 0.0370 chunk 164 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 overall best weight: 3.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1059 ASN A1175 GLN B 195 ASN C 166 GLN C 339 ASN C 400 GLN C 409 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 15751 Z= 0.337 Angle : 0.674 8.628 21547 Z= 0.357 Chirality : 0.046 0.155 2322 Planarity : 0.006 0.061 2602 Dihedral : 14.244 82.940 2458 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 4.13 % Allowed : 15.96 % Favored : 79.91 % 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: 0.48 (0.20), residues: 1758 helix: 0.90 (0.19), residues: 747 sheet: 0.92 (0.31), residues: 237 loop : -0.36 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 175 HIS 0.005 0.001 HIS A 805 PHE 0.030 0.003 PHE A 197 TYR 0.017 0.002 TYR A 649 ARG 0.006 0.001 ARG A 628 *********************** 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 426 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 362 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 31 residues processed: 398 average time/residue: 1.3364 time to fit residues: 583.7762 Evaluate side-chains 380 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 349 time to evaluate : 1.762 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 19 residues processed: 12 average time/residue: 0.7874 time to fit residues: 13.3300 ------------------------------------------------------------------------------- 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: 3.9990 chunk 123 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 A1157 ASN A1175 GLN B 195 ASN B 339 ASN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2088 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= 0.224 Angle : 0.592 8.120 21547 Z= 0.313 Chirality : 0.042 0.148 2322 Planarity : 0.005 0.044 2602 Dihedral : 14.264 82.851 2458 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 4.46 % Allowed : 16.93 % Favored : 78.62 % 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: 0.55 (0.20), residues: 1758 helix: 0.94 (0.19), residues: 749 sheet: 1.00 (0.31), residues: 239 loop : -0.33 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 175 HIS 0.003 0.001 HIS B 96 PHE 0.026 0.002 PHE A 197 TYR 0.014 0.002 TYR C 206 ARG 0.005 0.001 ARG A 657 *********************** 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 430 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 361 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 39 residues processed: 402 average time/residue: 1.2900 time to fit residues: 572.7717 Evaluate side-chains 392 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 353 time to evaluate : 1.690 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 26 residues processed: 13 average time/residue: 0.5433 time to fit residues: 10.9695 ------------------------------------------------------------------------------- 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: 3.9990 chunk 2 optimal weight: 0.0060 chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- 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 A1175 GLN B 187 HIS B 195 ASN B 323 HIS 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 15751 Z= 0.307 Angle : 0.656 8.623 21547 Z= 0.346 Chirality : 0.045 0.157 2322 Planarity : 0.006 0.053 2602 Dihedral : 14.408 87.453 2458 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.10 % Favored : 95.85 % Rotamer: Outliers : 5.04 % Allowed : 18.02 % Favored : 76.94 % 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: 0.27 (0.20), residues: 1758 helix: 0.68 (0.19), residues: 748 sheet: 0.91 (0.31), residues: 234 loop : -0.45 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 175 HIS 0.004 0.001 HIS B 96 PHE 0.029 0.002 PHE A 197 TYR 0.023 0.002 TYR A1166 ARG 0.004 0.001 ARG C 344 *********************** 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 425 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 347 time to evaluate : 1.777 Fit side-chains revert: symmetry clash outliers start: 78 outliers final: 40 residues processed: 397 average time/residue: 1.3150 time to fit residues: 574.8127 Evaluate side-chains 379 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 339 time to evaluate : 1.662 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 29 residues processed: 11 average time/residue: 0.6099 time to fit residues: 10.2972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 43 optimal weight: 0.0010 chunk 175 optimal weight: 7.9990 chunk 145 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 0.0050 overall best weight: 1.8004 ------------------------------------------------------------------------------- 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 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 Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15751 Z= 0.224 Angle : 0.605 8.188 21547 Z= 0.317 Chirality : 0.042 0.172 2322 Planarity : 0.005 0.043 2602 Dihedral : 14.356 86.382 2458 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 4.59 % Allowed : 19.38 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1758 helix: 0.80 (0.19), residues: 752 sheet: 1.05 (0.31), residues: 234 loop : -0.37 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 175 HIS 0.003 0.001 HIS A 734 PHE 0.026 0.002 PHE A 197 TYR 0.015 0.002 TYR A1166 ARG 0.003 0.000 ARG A 657 *********************** 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 425 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 354 time to evaluate : 1.795 Fit side-chains revert: symmetry clash outliers start: 71 outliers final: 43 residues processed: 405 average time/residue: 1.2453 time to fit residues: 557.9312 Evaluate side-chains 388 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 345 time to evaluate : 1.743 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 35 residues processed: 8 average time/residue: 0.6041 time to fit residues: 8.1660 ------------------------------------------------------------------------------- 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: 7.9990 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 0.3980 chunk 127 optimal weight: 5.9990 chunk 147 optimal weight: 0.0870 chunk 97 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 80 optimal weight: 0.0570 chunk 107 optimal weight: 6.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 659 HIS A 736 ASN A 843 GLN A 922 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 Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15751 Z= 0.157 Angle : 0.560 9.160 21547 Z= 0.292 Chirality : 0.040 0.143 2322 Planarity : 0.005 0.098 2602 Dihedral : 14.265 80.945 2458 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 3.94 % Allowed : 20.16 % Favored : 75.90 % 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: 0.71 (0.20), residues: 1758 helix: 1.02 (0.19), residues: 751 sheet: 1.23 (0.31), residues: 243 loop : -0.24 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 175 HIS 0.003 0.001 HIS A 659 PHE 0.022 0.001 PHE A 197 TYR 0.014 0.001 TYR A1166 ARG 0.012 0.000 ARG C 107 *********************** 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 427 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 366 time to evaluate : 1.770 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 41 residues processed: 411 average time/residue: 1.2927 time to fit residues: 587.3870 Evaluate side-chains 388 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 347 time to evaluate : 1.650 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 34 residues processed: 7 average time/residue: 0.6432 time to fit residues: 7.6304 ------------------------------------------------------------------------------- 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: 3.9990 chunk 104 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 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 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: 0.7830 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15751 Z= 0.207 Angle : 0.594 10.245 21547 Z= 0.309 Chirality : 0.041 0.148 2322 Planarity : 0.005 0.041 2602 Dihedral : 14.281 81.419 2458 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 4.13 % Allowed : 20.87 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1758 helix: 0.98 (0.19), residues: 752 sheet: 1.19 (0.31), residues: 243 loop : -0.30 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 175 HIS 0.004 0.001 HIS B 192 PHE 0.025 0.002 PHE A 197 TYR 0.014 0.002 TYR B 291 ARG 0.007 0.001 ARG A 628 *********************** 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 420 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 356 time to evaluate : 1.793 Fit side-chains revert: symmetry clash outliers start: 64 outliers final: 43 residues processed: 402 average time/residue: 1.2474 time to fit residues: 557.7461 Evaluate side-chains 385 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 342 time to evaluate : 1.716 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 35 residues processed: 8 average time/residue: 0.7339 time to fit residues: 9.1918 ------------------------------------------------------------------------------- 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: 7.9990 chunk 152 optimal weight: 8.9990 chunk 162 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 49 optimal weight: 0.1980 chunk 146 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 171 optimal weight: 0.0370 overall best weight: 1.6262 ------------------------------------------------------------------------------- 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 468 ASN A 564 GLN A 659 HIS A 736 ASN A 843 GLN A 922 GLN A1059 ASN A1157 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 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15751 Z= 0.212 Angle : 0.607 9.493 21547 Z= 0.316 Chirality : 0.042 0.155 2322 Planarity : 0.005 0.042 2602 Dihedral : 14.287 81.745 2458 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.36 % Rotamer: Outliers : 3.62 % Allowed : 21.38 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.20), residues: 1758 helix: 0.97 (0.19), residues: 746 sheet: 1.15 (0.31), residues: 243 loop : -0.34 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 175 HIS 0.004 0.001 HIS B 192 PHE 0.026 0.002 PHE A 197 TYR 0.014 0.002 TYR A 150 ARG 0.005 0.000 ARG A 361 *********************** 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 408 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 352 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 44 residues processed: 395 average time/residue: 1.2475 time to fit residues: 544.1229 Evaluate side-chains 390 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 346 time to evaluate : 1.716 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 34 residues processed: 10 average time/residue: 0.7706 time to fit residues: 11.2496 ------------------------------------------------------------------------------- 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: 5.9990 chunk 81 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 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 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15751 Z= 0.258 Angle : 0.650 9.239 21547 Z= 0.339 Chirality : 0.043 0.159 2322 Planarity : 0.005 0.048 2602 Dihedral : 14.374 86.362 2458 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.04 % Favored : 95.90 % Rotamer: Outliers : 3.17 % Allowed : 22.09 % Favored : 74.74 % 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: 0.42 (0.20), residues: 1758 helix: 0.79 (0.19), residues: 753 sheet: 1.10 (0.31), residues: 243 loop : -0.43 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 175 HIS 0.004 0.001 HIS B 192 PHE 0.027 0.002 PHE A 197 TYR 0.015 0.002 TYR B 291 ARG 0.010 0.001 ARG A 657 ********************** 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 398 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 349 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 37 residues processed: 386 average time/residue: 1.2956 time to fit residues: 552.6959 Evaluate side-chains 375 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 338 time to evaluate : 1.738 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 30 residues processed: 7 average time/residue: 0.5862 time to fit residues: 7.5680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 60 optimal weight: 0.0070 chunk 147 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 126 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 468 ASN A 564 GLN A 659 HIS A 736 ASN A 843 GLN A 922 GLN A1059 ASN A1175 GLN B 195 ASN B 261 GLN ** B 305 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 355 GLN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN C 422 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.126279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.118052 restraints weight = 26151.575| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.38 r_work: 0.3616 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15751 Z= 0.163 Angle : 0.579 10.402 21547 Z= 0.299 Chirality : 0.040 0.166 2322 Planarity : 0.004 0.040 2602 Dihedral : 14.222 77.746 2458 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.93 % Rotamer: Outliers : 2.65 % Allowed : 22.80 % Favored : 74.55 % 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: 0.72 (0.20), residues: 1758 helix: 1.11 (0.20), residues: 744 sheet: 1.23 (0.32), residues: 237 loop : -0.32 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 175 HIS 0.004 0.001 HIS A 659 PHE 0.022 0.001 PHE A 197 TYR 0.013 0.001 TYR A1166 ARG 0.009 0.000 ARG A 657 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8165.03 seconds wall clock time: 144 minutes 16.34 seconds (8656.34 seconds total)