Starting phenix.real_space_refine on Sun Jul 5 01:37:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qp9_18545/07_2026/8qp9_18545.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qp9_18545/07_2026/8qp9_18545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qp9_18545/07_2026/8qp9_18545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qp9_18545/07_2026/8qp9_18545.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qp9_18545/07_2026/8qp9_18545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qp9_18545/07_2026/8qp9_18545.map" } resolution = 4.1 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 189 5.49 5 S 14 5.16 5 C 14744 2.51 5 N 4794 2.21 5 O 5382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25123 Number of models: 1 Model: "" Number of chains: 17 Chain: "7" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 614 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 2, 'TRANS': 106} Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 9, 'HIS:plan': 2, 'ARG:plan': 7, 'PHE:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 7, 'GLU:plan': 10, 'ASN:plan1': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 187 Chain: "C" Number of atoms: 4924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 4924 Classifications: {'peptide': 852} Incomplete info: {'truncation_to_alanine': 533} Link IDs: {'PTRANS': 50, 'TRANS': 801} Unresolved non-hydrogen bonds: 1862 Unresolved non-hydrogen angles: 2371 Unresolved non-hydrogen dihedrals: 1502 Unresolved non-hydrogen chiralities: 179 Planarities with less than four sites: {'GLU:plan': 57, 'GLN:plan1': 26, 'TYR:plan': 13, 'ASP:plan': 57, 'PHE:plan': 21, 'ASN:plan1': 22, 'ARG:plan': 31, 'HIS:plan': 13, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 1060 Chain: "D" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 738 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 5, 'TRANS': 135} Unresolved non-hydrogen bonds: 451 Unresolved non-hydrogen angles: 579 Unresolved non-hydrogen dihedrals: 380 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'TYR:plan': 8, 'HIS:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 12, 'GLU:plan': 9, 'ARG:plan': 7, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 259 Chain: "J" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 216 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 4, 'TRANS': 37} Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "L" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 251 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 3, 'TRANS': 46} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 8, 'TYR:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "R" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 531 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 357 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 308 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 12, 'TRP:plan': 2, 'PHE:plan': 7, 'ARG:plan': 11, 'ASN:plan1': 4, 'TYR:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 208 Chain: "S" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 294 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5, 'PHE:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 101 Chain: "U" Number of atoms: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 2308 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 395} Link IDs: {'PTRANS': 23, 'TRANS': 432} Unresolved non-hydrogen bonds: 1515 Unresolved non-hydrogen angles: 1940 Unresolved non-hydrogen dihedrals: 1273 Unresolved non-hydrogen chiralities: 136 Planarities with less than four sites: {'ARG:plan': 18, 'HIS:plan': 17, 'TYR:plan': 23, 'ASP:plan': 23, 'ASN:plan1': 27, 'PHE:plan': 26, 'GLU:plan': 25, 'GLN:plan1': 21, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 862 Chain: "X" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 1, 'TRANS': 24} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 3, 'GLN:plan1': 2, 'ARG:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "G" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 503 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 490 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 13, 'HIS:plan': 3, 'ARG:plan': 13, 'TYR:plan': 4, 'PHE:plan': 4, 'TRP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 257 Chain: "6" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 795 Classifications: {'RNA': 37} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 19, 'rna3p_pyr': 15} Link IDs: {'rna2p': 3, 'rna3p': 33} Chain breaks: 1 Chain: "5" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1496 Classifications: {'RNA': 71} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 25, 'rna3p_pyr': 32} Link IDs: {'rna2p': 12, 'rna3p': 58} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "4" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1617 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 31, 'rna3p_pyr': 31} Link IDs: {'rna2p': 14, 'rna3p': 61} Chain breaks: 2 Chain: "A" Number of atoms: 9845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1916, 9845 Classifications: {'peptide': 1916} Incomplete info: {'truncation_to_alanine': 1610} Link IDs: {'PTRANS': 106, 'TRANS': 1809} Chain breaks: 4 Unresolved non-hydrogen bonds: 6412 Unresolved non-hydrogen angles: 8250 Unresolved non-hydrogen dihedrals: 5437 Unresolved non-hydrogen chiralities: 544 Planarities with less than four sites: {'GLU:plan': 111, 'ASP:plan': 111, 'HIS:plan': 56, 'ARG:plan': 125, 'TYR:plan': 82, 'ASN:plan1': 100, 'TRP:plan': 49, 'GLN:plan1': 82, 'PHE:plan': 81} Unresolved non-hydrogen planarities: 3811 Chain: "N" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 760 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'PTRANS': 6, 'TRANS': 145} Chain breaks: 2 Unresolved non-hydrogen bonds: 473 Unresolved non-hydrogen angles: 593 Unresolved non-hydrogen dihedrals: 386 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'ARG:plan': 13, 'PHE:plan': 4, 'ASP:plan': 15, 'ASN:plan1': 5, 'TYR:plan': 6, 'GLU:plan': 18, 'GLN:plan1': 7, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 300 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.60, per 1000 atoms: 0.22 Number of scatterers: 25123 At special positions: 0 Unit cell: (206.55, 155.25, 140.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 189 15.00 O 5382 8.00 N 4794 7.00 C 14744 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.33 Conformation dependent library (CDL) restraints added in 1.3 seconds 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7654 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 34 sheets defined 46.9% alpha, 8.9% beta 49 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain '7' and resid 461 through 472 removed outlier: 4.013A pdb=" N SER 7 465 " --> pdb=" O ASP 7 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 273 Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 298 through 311 Processing helix chain 'B' and resid 314 through 324 removed outlier: 4.278A pdb=" N ILE B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.563A pdb=" N ALA B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 364 Processing helix chain 'C' and resid 115 through 125 Processing helix chain 'C' and resid 141 through 154 Processing helix chain 'C' and resid 171 through 178 removed outlier: 3.518A pdb=" N GLY C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 220 removed outlier: 4.079A pdb=" N VAL C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG C 220 " --> pdb=" O THR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 259 through 266 removed outlier: 3.993A pdb=" N LEU C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 293 removed outlier: 3.834A pdb=" N TYR C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 332 Processing helix chain 'C' and resid 335 through 341 Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 373 through 387 removed outlier: 3.510A pdb=" N LEU C 377 " --> pdb=" O ILE C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 400 Proline residue: C 393 - end of helix Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.760A pdb=" N LEU C 410 " --> pdb=" O GLU C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 438 removed outlier: 3.591A pdb=" N VAL C 431 " --> pdb=" O PHE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 459 through 468 removed outlier: 3.590A pdb=" N CYS C 468 " --> pdb=" O ALA C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 522 removed outlier: 4.395A pdb=" N ASP C 521 " --> pdb=" O ASP C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 599 through 614 Processing helix chain 'C' and resid 634 through 645 Processing helix chain 'C' and resid 679 through 682 removed outlier: 4.164A pdb=" N LYS C 682 " --> pdb=" O PRO C 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 679 through 682' Processing helix chain 'C' and resid 695 through 702 Processing helix chain 'C' and resid 710 through 721 removed outlier: 3.537A pdb=" N LYS C 721 " --> pdb=" O PHE C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 730 Processing helix chain 'C' and resid 755 through 762 removed outlier: 3.511A pdb=" N VAL C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 777 Processing helix chain 'C' and resid 807 through 823 Processing helix chain 'C' and resid 842 through 852 removed outlier: 3.936A pdb=" N ARG C 852 " --> pdb=" O THR C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 880 No H-bonds generated for 'chain 'C' and resid 878 through 880' Processing helix chain 'C' and resid 882 through 891 removed outlier: 3.537A pdb=" N THR C 891 " --> pdb=" O LEU C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 941 removed outlier: 3.760A pdb=" N GLU C 932 " --> pdb=" O HIS C 928 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 21 removed outlier: 3.679A pdb=" N GLU D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 48 Processing helix chain 'D' and resid 51 through 54 removed outlier: 4.087A pdb=" N ASN D 54 " --> pdb=" O LYS D 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 51 through 54' Processing helix chain 'D' and resid 67 through 73 Processing helix chain 'D' and resid 108 through 126 Processing helix chain 'J' and resid 441 through 466 Processing helix chain 'L' and resid 359 through 366 Processing helix chain 'R' and resid 372 through 376 Processing helix chain 'R' and resid 431 through 442 Processing helix chain 'R' and resid 461 through 473 removed outlier: 4.014A pdb=" N VAL R 467 " --> pdb=" O ASN R 463 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU R 473 " --> pdb=" O LYS R 469 " (cutoff:3.500A) Processing helix chain 'S' and resid 721 through 735 Processing helix chain 'S' and resid 739 through 759 removed outlier: 3.619A pdb=" N MET S 759 " --> pdb=" O LEU S 755 " (cutoff:3.500A) Processing helix chain 'U' and resid 106 through 111 removed outlier: 3.695A pdb=" N ILE U 111 " --> pdb=" O LEU U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 116 Processing helix chain 'U' and resid 150 through 160 Processing helix chain 'U' and resid 183 through 185 No H-bonds generated for 'chain 'U' and resid 183 through 185' Processing helix chain 'U' and resid 186 through 194 removed outlier: 3.694A pdb=" N THR U 190 " --> pdb=" O LEU U 186 " (cutoff:3.500A) Processing helix chain 'U' and resid 204 through 208 removed outlier: 4.493A pdb=" N ASP U 207 " --> pdb=" O ALA U 204 " (cutoff:3.500A) Processing helix chain 'U' and resid 234 through 245 Processing helix chain 'U' and resid 247 through 255 Processing helix chain 'U' and resid 257 through 262 removed outlier: 4.340A pdb=" N ASN U 262 " --> pdb=" O ASP U 258 " (cutoff:3.500A) Processing helix chain 'U' and resid 271 through 286 removed outlier: 3.830A pdb=" N VAL U 275 " --> pdb=" O MET U 271 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY U 279 " --> pdb=" O VAL U 275 " (cutoff:3.500A) Processing helix chain 'U' and resid 297 through 307 Processing helix chain 'U' and resid 319 through 336 removed outlier: 3.763A pdb=" N GLY U 336 " --> pdb=" O HIS U 332 " (cutoff:3.500A) Processing helix chain 'U' and resid 344 through 351 removed outlier: 3.608A pdb=" N GLN U 351 " --> pdb=" O THR U 347 " (cutoff:3.500A) Processing helix chain 'U' and resid 367 through 377 Processing helix chain 'U' and resid 416 through 421 Processing helix chain 'U' and resid 422 through 424 No H-bonds generated for 'chain 'U' and resid 422 through 424' Processing helix chain 'U' and resid 486 through 490 removed outlier: 3.540A pdb=" N VAL U 489 " --> pdb=" O SER U 486 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN U 490 " --> pdb=" O GLU U 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 486 through 490' Processing helix chain 'U' and resid 539 through 544 removed outlier: 3.775A pdb=" N THR U 544 " --> pdb=" O PRO U 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 255 Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 308 through 315 Processing helix chain 'G' and resid 318 through 328 Processing helix chain 'G' and resid 329 through 353 Processing helix chain 'A' and resid 62 through 73 removed outlier: 4.048A pdb=" N VAL A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 136 through 158 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.539A pdb=" N GLU A 291 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.822A pdb=" N PHE A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 405 removed outlier: 4.120A pdb=" N ALA A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ASN A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 427 through 433 Processing helix chain 'A' and resid 440 through 460 Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 489 through 508 Processing helix chain 'A' and resid 531 through 538 Processing helix chain 'A' and resid 541 through 566 Processing helix chain 'A' and resid 570 through 583 Processing helix chain 'A' and resid 585 through 590 Processing helix chain 'A' and resid 597 through 617 removed outlier: 4.364A pdb=" N GLN A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 656 Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 680 through 697 Processing helix chain 'A' and resid 704 through 721 removed outlier: 4.008A pdb=" N THR A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 764 Processing helix chain 'A' and resid 768 through 798 Processing helix chain 'A' and resid 802 through 821 Processing helix chain 'A' and resid 834 through 848 Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 873 through 888 Processing helix chain 'A' and resid 912 through 934 Processing helix chain 'A' and resid 947 through 962 removed outlier: 3.611A pdb=" N ASN A 960 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 962 " --> pdb=" O GLY A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 998 Processing helix chain 'A' and resid 1002 through 1014 Processing helix chain 'A' and resid 1036 through 1054 Processing helix chain 'A' and resid 1054 through 1062 Processing helix chain 'A' and resid 1076 through 1081 removed outlier: 3.515A pdb=" N ALA A1081 " --> pdb=" O ILE A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1117 Processing helix chain 'A' and resid 1123 through 1127 removed outlier: 3.661A pdb=" N GLY A1127 " --> pdb=" O ASN A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1161 removed outlier: 3.628A pdb=" N LEU A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1250 Processing helix chain 'A' and resid 1255 through 1274 Processing helix chain 'A' and resid 1276 through 1281 removed outlier: 4.104A pdb=" N ASN A1280 " --> pdb=" O GLU A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1304 Processing helix chain 'A' and resid 1312 through 1318 removed outlier: 4.150A pdb=" N PHE A1316 " --> pdb=" O PRO A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1340 removed outlier: 3.795A pdb=" N LEU A1340 " --> pdb=" O GLN A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1372 removed outlier: 4.272A pdb=" N TYR A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A1372 " --> pdb=" O LEU A1368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1367 through 1372' Processing helix chain 'A' and resid 1374 through 1399 removed outlier: 3.507A pdb=" N GLN A1399 " --> pdb=" O GLU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.594A pdb=" N TYR A1432 " --> pdb=" O HIS A1428 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP A1433 " --> pdb=" O THR A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1443 Processing helix chain 'A' and resid 1444 through 1446 No H-bonds generated for 'chain 'A' and resid 1444 through 1446' Processing helix chain 'A' and resid 1467 through 1478 Processing helix chain 'A' and resid 1479 through 1487 removed outlier: 3.764A pdb=" N HIS A1487 " --> pdb=" O GLY A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1519 through 1538 Proline residue: A1530 - end of helix Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1566 through 1577 Processing helix chain 'A' and resid 1580 through 1600 removed outlier: 3.878A pdb=" N LYS A1584 " --> pdb=" O HIS A1580 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU A1600 " --> pdb=" O VAL A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1619 Processing helix chain 'A' and resid 1675 through 1689 removed outlier: 3.609A pdb=" N THR A1689 " --> pdb=" O LEU A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1737 Processing helix chain 'A' and resid 1737 through 1751 Processing helix chain 'A' and resid 1767 through 1773 removed outlier: 3.892A pdb=" N LEU A1771 " --> pdb=" O TYR A1768 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A1772 " --> pdb=" O GLY A1769 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A1773 " --> pdb=" O GLU A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1782 through 1786 removed outlier: 3.943A pdb=" N TYR A1786 " --> pdb=" O THR A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1828 removed outlier: 3.540A pdb=" N TRP A1827 " --> pdb=" O HIS A1823 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1852 removed outlier: 3.562A pdb=" N ALA A1837 " --> pdb=" O LEU A1833 " (cutoff:3.500A) Processing helix chain 'A' and resid 1853 through 1857 Processing helix chain 'A' and resid 1865 through 1867 No H-bonds generated for 'chain 'A' and resid 1865 through 1867' Processing helix chain 'A' and resid 1868 through 1876 Processing helix chain 'A' and resid 1892 through 1899 removed outlier: 3.666A pdb=" N ALA A1895 " --> pdb=" O PRO A1892 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS A1896 " --> pdb=" O PHE A1893 " (cutoff:3.500A) Processing helix chain 'A' and resid 1901 through 1909 Processing helix chain 'A' and resid 1928 through 1946 removed outlier: 3.594A pdb=" N ASN A1946 " --> pdb=" O ALA A1942 " (cutoff:3.500A) Processing helix chain 'A' and resid 1947 through 1955 Processing helix chain 'A' and resid 1972 through 1996 Processing helix chain 'A' and resid 2003 through 2013 Processing helix chain 'N' and resid 19 through 24 removed outlier: 3.746A pdb=" N GLY N 22 " --> pdb=" O PRO N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 112 Processing helix chain 'N' and resid 116 through 132 Processing helix chain 'N' and resid 137 through 150 removed outlier: 4.138A pdb=" N ASP N 144 " --> pdb=" O GLN N 140 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU N 145 " --> pdb=" O GLN N 141 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA N 150 " --> pdb=" O LYS N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 260 removed outlier: 4.001A pdb=" N ILE N 243 " --> pdb=" O ASP N 239 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY N 244 " --> pdb=" O MET N 240 " (cutoff:3.500A) Processing helix chain 'N' and resid 269 through 276 Processing helix chain 'N' and resid 277 through 280 removed outlier: 3.956A pdb=" N MET N 280 " --> pdb=" O LEU N 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 277 through 280' Processing sheet with id=AA1, first strand: chain 'C' and resid 184 through 191 removed outlier: 3.621A pdb=" N THR C 184 " --> pdb=" O ASP C 204 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP C 204 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG C 130 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N MET C 203 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL C 132 " --> pdb=" O MET C 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 228 through 230 removed outlier: 6.362A pdb=" N ILE C 229 " --> pdb=" O ASN C 258 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 348 through 350 Processing sheet with id=AA4, first strand: chain 'C' and resid 477 through 483 removed outlier: 5.532A pdb=" N THR C 478 " --> pdb=" O ARG C 495 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ARG C 495 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 551 " --> pdb=" O TRP C 531 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TRP C 531 " --> pdb=" O LEU C 551 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE C 539 " --> pdb=" O ILE C 532 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 501 through 502 Processing sheet with id=AA6, first strand: chain 'C' and resid 523 through 526 removed outlier: 3.585A pdb=" N GLN C 523 " --> pdb=" O VAL C 509 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 619 through 621 removed outlier: 3.899A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 619 through 621 removed outlier: 3.899A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 674 through 677 removed outlier: 4.203A pdb=" N CYS C 674 " --> pdb=" O MET C 687 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET C 687 " --> pdb=" O CYS C 674 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS C 684 " --> pdb=" O ALA C 794 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 794 " --> pdb=" O LYS C 684 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 732 through 734 removed outlier: 6.691A pdb=" N LEU C 745 " --> pdb=" O TRP C 733 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 856 through 859 removed outlier: 6.289A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU C 829 " --> pdb=" O TRP C 904 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TRP C 904 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N TYR C 831 " --> pdb=" O HIS C 902 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 56 through 60 removed outlier: 6.218A pdb=" N VAL D 25 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TYR D 59 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL D 27 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D 26 " --> pdb=" O PHE D 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 91 through 92 removed outlier: 6.245A pdb=" N MET D 91 " --> pdb=" O VAL D 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'R' and resid 425 through 429 removed outlier: 4.133A pdb=" N GLY R 386 " --> pdb=" O LYS R 453 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS R 453 " --> pdb=" O GLY R 386 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'U' and resid 142 through 144 Processing sheet with id=AB7, first strand: chain 'U' and resid 213 through 214 Processing sheet with id=AB8, first strand: chain 'U' and resid 352 through 354 Processing sheet with id=AB9, first strand: chain 'U' and resid 357 through 358 Processing sheet with id=AC1, first strand: chain 'U' and resid 391 through 392 removed outlier: 6.766A pdb=" N ILE U 550 " --> pdb=" O ASN U 503 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASN U 503 " --> pdb=" O ILE U 550 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE U 552 " --> pdb=" O ILE U 501 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 391 through 392 removed outlier: 6.766A pdb=" N ILE U 550 " --> pdb=" O ASN U 503 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASN U 503 " --> pdb=" O ILE U 550 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE U 552 " --> pdb=" O ILE U 501 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 413 through 415 removed outlier: 6.851A pdb=" N VAL U 414 " --> pdb=" O ASN U 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'U' and resid 428 through 431 Processing sheet with id=AC5, first strand: chain 'A' and resid 127 through 128 Processing sheet with id=AC6, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AC7, first strand: chain 'A' and resid 516 through 518 Processing sheet with id=AC8, first strand: chain 'A' and resid 906 through 910 removed outlier: 3.896A pdb=" N VAL A 906 " --> pdb=" O MET A 899 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL A 894 " --> pdb=" O ASN A1018 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1085 through 1088 removed outlier: 6.193A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1185 through 1189 removed outlier: 3.650A pdb=" N MET A1189 " --> pdb=" O PHE A1192 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1343 through 1344 Processing sheet with id=AD3, first strand: chain 'A' and resid 1501 through 1503 removed outlier: 3.591A pdb=" N PHE A1502 " --> pdb=" O TYR A1754 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1552 through 1554 Processing sheet with id=AD5, first strand: chain 'A' and resid 1609 through 1611 removed outlier: 3.502A pdb=" N LEU A1631 " --> pdb=" O TYR A1660 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLN A1658 " --> pdb=" O ALA A1633 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N TYR A1635 " --> pdb=" O THR A1656 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N THR A1656 " --> pdb=" O TYR A1635 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 1788 through 1791 removed outlier: 3.662A pdb=" N LYS A1801 " --> pdb=" O THR A1789 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A1791 " --> pdb=" O THR A1799 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 1805 through 1811 removed outlier: 3.536A pdb=" N LYS A1820 " --> pdb=" O ILE A1807 " (cutoff:3.500A) 1407 hydrogen bonds defined for protein. 4029 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 115 hydrogen bonds 198 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 7.47 Time building geometry restraints manager: 2.95 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: 8384 1.34 - 1.45: 3404 1.45 - 1.57: 13665 1.57 - 1.69: 366 1.69 - 1.81: 19 Bond restraints: 25838 Sorted by residual: bond pdb=" O12 IHP A2401 " pdb=" P2 IHP A2401 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" O15 IHP A2401 " pdb=" P5 IHP A2401 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O16 IHP A2401 " pdb=" P6 IHP A2401 " ideal model delta sigma weight residual 1.672 1.605 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" O14 IHP A2401 " pdb=" P4 IHP A2401 " ideal model delta sigma weight residual 1.671 1.608 0.063 2.00e-02 2.50e+03 9.79e+00 bond pdb=" O13 IHP A2401 " pdb=" P3 IHP A2401 " ideal model delta sigma weight residual 1.669 1.608 0.061 2.00e-02 2.50e+03 9.38e+00 ... (remaining 25833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 36111 1.40 - 2.80: 525 2.80 - 4.20: 119 4.20 - 5.60: 34 5.60 - 7.00: 3 Bond angle restraints: 36792 Sorted by residual: angle pdb=" C1' C 5 23 " pdb=" N1 C 5 23 " pdb=" C2 C 5 23 " ideal model delta sigma weight residual 118.80 125.15 -6.35 1.10e+00 8.26e-01 3.33e+01 angle pdb=" N1 C 5 23 " pdb=" C2 C 5 23 " pdb=" O2 C 5 23 " ideal model delta sigma weight residual 118.90 122.06 -3.16 6.00e-01 2.78e+00 2.78e+01 angle pdb=" O2 C 5 23 " pdb=" C2 C 5 23 " pdb=" N3 C 5 23 " ideal model delta sigma weight residual 121.90 118.80 3.10 7.00e-01 2.04e+00 1.96e+01 angle pdb=" C1' C 5 23 " pdb=" N1 C 5 23 " pdb=" C6 C 5 23 " ideal model delta sigma weight residual 120.80 116.04 4.76 1.20e+00 6.94e-01 1.58e+01 angle pdb=" C2 C 5 23 " pdb=" N1 C 5 23 " pdb=" C6 C 5 23 " ideal model delta sigma weight residual 120.30 118.80 1.50 4.00e-01 6.25e+00 1.40e+01 ... (remaining 36787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 15086 36.00 - 71.99: 421 71.99 - 107.99: 64 107.99 - 143.98: 7 143.98 - 179.98: 5 Dihedral angle restraints: 15583 sinusoidal: 3909 harmonic: 11674 Sorted by residual: dihedral pdb=" O4' C 5 23 " pdb=" C1' C 5 23 " pdb=" N1 C 5 23 " pdb=" C2 C 5 23 " ideal model delta sinusoidal sigma weight residual 200.00 69.86 130.14 1 1.50e+01 4.44e-03 7.02e+01 dihedral pdb=" O4' C 5 38 " pdb=" C1' C 5 38 " pdb=" N1 C 5 38 " pdb=" C2 C 5 38 " ideal model delta sinusoidal sigma weight residual 232.00 52.02 179.98 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C 5 71 " pdb=" C1' C 5 71 " pdb=" N1 C 5 71 " pdb=" C2 C 5 71 " ideal model delta sinusoidal sigma weight residual 232.00 59.82 172.18 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 15580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 4848 1.007 - 2.014: 0 2.014 - 3.021: 0 3.021 - 4.027: 0 4.027 - 5.034: 4 Chirality restraints: 4852 Sorted by residual: chirality pdb=" C2 IHP A2401 " pdb=" C1 IHP A2401 " pdb=" C3 IHP A2401 " pdb=" O12 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.52 2.52 -5.03 2.00e-01 2.50e+01 6.34e+02 chirality pdb=" C5 IHP A2401 " pdb=" C4 IHP A2401 " pdb=" C6 IHP A2401 " pdb=" O15 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.42 2.48 -4.90 2.00e-01 2.50e+01 6.00e+02 chirality pdb=" C3 IHP A2401 " pdb=" C2 IHP A2401 " pdb=" C4 IHP A2401 " pdb=" O13 IHP A2401 " both_signs ideal model delta sigma weight residual False -2.34 2.46 -4.80 2.00e-01 2.50e+01 5.77e+02 ... (remaining 4849 not shown) Planarity restraints: 4478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 132 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.23e+00 pdb=" N PRO D 133 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 133 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 133 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO U 248 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.10e+00 pdb=" N PRO U 249 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO U 249 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO U 249 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY N 92 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO N 93 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO N 93 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO N 93 " 0.027 5.00e-02 4.00e+02 ... (remaining 4475 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4305 2.76 - 3.30: 24174 3.30 - 3.83: 42272 3.83 - 4.37: 39167 4.37 - 4.90: 67805 Nonbonded interactions: 177723 Sorted by model distance: nonbonded pdb=" O2' A 5 47 " pdb=" O5' A 5 48 " model vdw 2.226 3.040 nonbonded pdb=" O HIS C 451 " pdb=" NH1 ARG C 578 " model vdw 2.250 3.120 nonbonded pdb=" O SER C 183 " pdb=" OH TYR C 482 " model vdw 2.252 3.040 nonbonded pdb=" N2 G 5 8 " pdb=" O2 U 5 74 " model vdw 2.293 3.120 nonbonded pdb=" N6 A 6 69 " pdb=" O4 U 4 5 " model vdw 2.297 3.120 ... (remaining 177718 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.400 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 28.140 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 25838 Z= 0.129 Angle : 0.476 7.002 36792 Z= 0.290 Chirality : 0.145 5.034 4852 Planarity : 0.004 0.072 4478 Dihedral : 16.826 179.978 7929 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 3983 helix: 2.13 (0.13), residues: 1702 sheet: -2.03 (0.26), residues: 405 loop : -1.34 (0.16), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 529 TYR 0.021 0.001 TYR C 327 PHE 0.011 0.001 PHE C 323 TRP 0.014 0.001 TRP C 531 HIS 0.001 0.000 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.13 (25838) covalent geometry : angle 0.47621 / 0.29 (36792) hydrogen bonds : bond 0.18168 / 13.29 ( 1506) hydrogen bonds : angle 7.03644 / 5.24 ( 4227) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.824 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1207 time to fit residues: 28.5883 Evaluate side-chains 118 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 overall best weight: 9.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.088601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.071943 restraints weight = 129405.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.071389 restraints weight = 191328.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.071630 restraints weight = 172537.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.071368 restraints weight = 133329.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.071448 restraints weight = 127373.469| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.096 25838 Z= 0.479 Angle : 0.918 21.247 36792 Z= 0.525 Chirality : 0.060 1.078 4852 Planarity : 0.008 0.075 4478 Dihedral : 17.510 177.115 6883 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.80 % Favored : 89.08 % Rotamer: Outliers : 1.18 % Allowed : 9.00 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.13), residues: 3983 helix: -0.48 (0.11), residues: 1755 sheet: -2.66 (0.25), residues: 421 loop : -2.26 (0.15), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG C 250 TYR 0.031 0.002 TYR C 636 PHE 0.047 0.003 PHE A 387 TRP 0.022 0.002 TRP A 637 HIS 0.014 0.005 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00878 / 0.48 (25838) covalent geometry : angle 0.91803 / 0.53 (36792) hydrogen bonds : bond 0.08573 / 6.13 ( 1506) hydrogen bonds : angle 6.62788 / 4.95 ( 4227) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.799 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 119 average time/residue: 0.1192 time to fit residues: 26.8680 Evaluate side-chains 113 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 264 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 310 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 362 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 17 optimal weight: 0.4980 chunk 273 optimal weight: 10.0000 chunk 312 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 344 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.091399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.074840 restraints weight = 128502.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.074487 restraints weight = 177888.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.074283 restraints weight = 151982.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.074016 restraints weight = 135020.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.074143 restraints weight = 123423.099| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25838 Z= 0.135 Angle : 0.525 12.738 36792 Z= 0.288 Chirality : 0.043 0.430 4852 Planarity : 0.005 0.057 4478 Dihedral : 16.997 177.918 6883 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.14), residues: 3983 helix: 1.13 (0.12), residues: 1760 sheet: -2.40 (0.25), residues: 425 loop : -1.74 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 250 TYR 0.021 0.001 TYR C 327 PHE 0.013 0.001 PHE A1088 TRP 0.013 0.001 TRP A 637 HIS 0.003 0.001 HIS C 627 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 (25838) covalent geometry : angle 0.52476 / 0.29 (36792) hydrogen bonds : bond 0.05395 / 3.88 ( 1506) hydrogen bonds : angle 5.03138 / 3.77 ( 4227) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.886 Fit side-chains REVERT: C 177 ARG cc_start: 0.7742 (tpt90) cc_final: 0.7511 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1273 time to fit residues: 30.7971 Evaluate side-chains 116 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 114 optimal weight: 0.0040 chunk 170 optimal weight: 0.9980 chunk 297 optimal weight: 0.9990 chunk 374 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 328 optimal weight: 7.9990 chunk 324 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 341 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.092366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.075857 restraints weight = 129470.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.075640 restraints weight = 174013.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.075430 restraints weight = 150808.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.075188 restraints weight = 125815.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.075313 restraints weight = 118720.490| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25838 Z= 0.092 Angle : 0.442 6.728 36792 Z= 0.241 Chirality : 0.040 0.280 4852 Planarity : 0.004 0.051 4478 Dihedral : 16.673 179.652 6883 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3983 helix: 1.97 (0.13), residues: 1758 sheet: -2.17 (0.25), residues: 437 loop : -1.43 (0.16), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1141 TYR 0.009 0.001 TYR C 482 PHE 0.013 0.001 PHE C 427 TRP 0.013 0.001 TRP C 531 HIS 0.003 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00175 / 0.09 (25838) covalent geometry : angle 0.44204 / 0.24 (36792) hydrogen bonds : bond 0.04133 / 3.02 ( 1506) hydrogen bonds : angle 4.19691 / 3.16 ( 4227) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.825 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1118 time to fit residues: 27.0053 Evaluate side-chains 118 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 372 optimal weight: 7.9990 chunk 410 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 256 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 199 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 407 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.091732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.075230 restraints weight = 128745.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.074854 restraints weight = 173790.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.074598 restraints weight = 157522.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.074355 restraints weight = 136316.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.074548 restraints weight = 122936.122| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25838 Z= 0.127 Angle : 0.461 6.907 36792 Z= 0.253 Chirality : 0.041 0.276 4852 Planarity : 0.004 0.050 4478 Dihedral : 16.696 178.774 6883 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.14), residues: 3983 helix: 1.91 (0.13), residues: 1758 sheet: -2.11 (0.25), residues: 435 loop : -1.44 (0.16), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 578 TYR 0.012 0.001 TYR C 275 PHE 0.015 0.001 PHE A 387 TRP 0.009 0.001 TRP A 637 HIS 0.003 0.001 HIS C 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.13 (25838) covalent geometry : angle 0.46088 / 0.25 (36792) hydrogen bonds : bond 0.04317 / 3.14 ( 1506) hydrogen bonds : angle 4.29100 / 3.23 ( 4227) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.877 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1117 time to fit residues: 25.9908 Evaluate side-chains 115 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 400 optimal weight: 30.0000 chunk 312 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 259 optimal weight: 0.9990 chunk 354 optimal weight: 0.0970 chunk 288 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 152 GLN C 245 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.091367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.074707 restraints weight = 127770.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.074242 restraints weight = 174355.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.074195 restraints weight = 171691.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.073881 restraints weight = 149459.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.074029 restraints weight = 133493.694| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25838 Z= 0.152 Angle : 0.487 7.117 36792 Z= 0.270 Chirality : 0.042 0.267 4852 Planarity : 0.004 0.048 4478 Dihedral : 16.796 178.439 6883 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3983 helix: 1.74 (0.13), residues: 1756 sheet: -2.16 (0.26), residues: 427 loop : -1.52 (0.16), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 578 TYR 0.016 0.001 TYR C 275 PHE 0.014 0.001 PHE A1088 TRP 0.012 0.001 TRP A 637 HIS 0.006 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (25838) covalent geometry : angle 0.48724 / 0.27 (36792) hydrogen bonds : bond 0.04432 / 3.22 ( 1506) hydrogen bonds : angle 4.45386 / 3.35 ( 4227) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.875 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1151 time to fit residues: 26.2258 Evaluate side-chains 114 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 30 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 212 optimal weight: 0.0770 chunk 317 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 345 optimal weight: 0.8980 chunk 255 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 chunk 152 optimal weight: 9.9990 chunk 376 optimal weight: 8.9990 overall best weight: 3.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.090968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.074422 restraints weight = 127938.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.074143 restraints weight = 186379.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.073877 restraints weight = 162607.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.073506 restraints weight = 150555.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.073620 restraints weight = 149808.024| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25838 Z= 0.186 Angle : 0.520 7.238 36792 Z= 0.291 Chirality : 0.043 0.265 4852 Planarity : 0.005 0.050 4478 Dihedral : 16.897 178.530 6883 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3983 helix: 1.50 (0.13), residues: 1756 sheet: -2.30 (0.25), residues: 433 loop : -1.62 (0.16), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 578 TYR 0.019 0.001 TYR C 275 PHE 0.025 0.001 PHE A 387 TRP 0.012 0.001 TRP A 637 HIS 0.006 0.002 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.19 (25838) covalent geometry : angle 0.51957 / 0.29 (36792) hydrogen bonds : bond 0.04649 / 3.39 ( 1506) hydrogen bonds : angle 4.66814 / 3.51 ( 4227) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.906 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1138 time to fit residues: 25.8372 Evaluate side-chains 112 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 29 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 234 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 321 optimal weight: 20.0000 chunk 117 optimal weight: 30.0000 chunk 199 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.089832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.073420 restraints weight = 128536.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.073042 restraints weight = 196164.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.073170 restraints weight = 190915.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.073070 restraints weight = 149900.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.073149 restraints weight = 141442.550| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 25838 Z= 0.280 Angle : 0.631 7.769 36792 Z= 0.364 Chirality : 0.046 0.268 4852 Planarity : 0.006 0.057 4478 Dihedral : 17.258 177.058 6883 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.14), residues: 3983 helix: 0.59 (0.12), residues: 1752 sheet: -2.65 (0.25), residues: 429 loop : -1.88 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 578 TYR 0.054 0.002 TYR C 378 PHE 0.032 0.002 PHE A 387 TRP 0.015 0.001 TRP A 406 HIS 0.011 0.003 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.28 (25838) covalent geometry : angle 0.63106 / 0.36 (36792) hydrogen bonds : bond 0.05640 / 4.11 ( 1506) hydrogen bonds : angle 5.38059 / 4.05 ( 4227) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.878 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1120 time to fit residues: 24.9720 Evaluate side-chains 111 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 88 optimal weight: 2.9990 chunk 385 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 367 optimal weight: 1.9990 chunk 371 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 386 optimal weight: 0.0020 chunk 93 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 261 optimal weight: 0.5980 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.091887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.075411 restraints weight = 127874.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.075157 restraints weight = 187652.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.074712 restraints weight = 147237.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.074420 restraints weight = 138003.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.074530 restraints weight = 135809.077| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25838 Z= 0.109 Angle : 0.472 7.027 36792 Z= 0.260 Chirality : 0.041 0.276 4852 Planarity : 0.004 0.055 4478 Dihedral : 16.919 179.673 6883 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3983 helix: 1.73 (0.13), residues: 1753 sheet: -2.37 (0.25), residues: 433 loop : -1.53 (0.16), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 645 TYR 0.036 0.001 TYR C 327 PHE 0.017 0.001 PHE C 323 TRP 0.013 0.001 TRP C 531 HIS 0.007 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.11 (25838) covalent geometry : angle 0.47167 / 0.26 (36792) hydrogen bonds : bond 0.04069 / 2.97 ( 1506) hydrogen bonds : angle 4.40204 / 3.32 ( 4227) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.785 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1113 time to fit residues: 26.2771 Evaluate side-chains 117 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 238 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 340 optimal weight: 0.1980 chunk 248 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 396 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 271 optimal weight: 0.0030 chunk 385 optimal weight: 6.9990 overall best weight: 2.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.091327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.074869 restraints weight = 127753.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.074604 restraints weight = 182656.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.074208 restraints weight = 156323.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.073929 restraints weight = 144406.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.074076 restraints weight = 126418.095| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25838 Z= 0.139 Angle : 0.479 7.122 36792 Z= 0.265 Chirality : 0.042 0.267 4852 Planarity : 0.004 0.050 4478 Dihedral : 16.903 179.298 6883 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3983 helix: 1.70 (0.13), residues: 1761 sheet: -2.30 (0.25), residues: 423 loop : -1.54 (0.16), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 578 TYR 0.021 0.001 TYR C 327 PHE 0.016 0.001 PHE A 387 TRP 0.010 0.001 TRP A 637 HIS 0.007 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (25838) covalent geometry : angle 0.47931 / 0.26 (36792) hydrogen bonds : bond 0.04210 / 3.08 ( 1506) hydrogen bonds : angle 4.42012 / 3.34 ( 4227) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.893 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1097 time to fit residues: 25.5550 Evaluate side-chains 116 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 114 optimal weight: 0.0570 chunk 373 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 199 optimal weight: 10.0000 chunk 213 optimal weight: 0.0570 chunk 165 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.092532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.076102 restraints weight = 127594.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.075848 restraints weight = 168998.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.075353 restraints weight = 147679.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.075108 restraints weight = 143494.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.075250 restraints weight = 129608.600| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25838 Z= 0.090 Angle : 0.438 6.928 36792 Z= 0.237 Chirality : 0.040 0.281 4852 Planarity : 0.004 0.055 4478 Dihedral : 16.741 179.936 6883 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3983 helix: 2.21 (0.13), residues: 1760 sheet: -2.15 (0.26), residues: 426 loop : -1.35 (0.16), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 645 TYR 0.023 0.001 TYR C 327 PHE 0.012 0.001 PHE C 323 TRP 0.014 0.001 TRP C 531 HIS 0.006 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00172 / 0.09 (25838) covalent geometry : angle 0.43790 / 0.24 (36792) hydrogen bonds : bond 0.03735 / 2.74 ( 1506) hydrogen bonds : angle 3.94010 / 2.97 ( 4227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3271.43 seconds wall clock time: 56 minutes 58.07 seconds (3418.07 seconds total)