Starting phenix.real_space_refine on Mon Aug 25 02:49:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qp9_18545/08_2025/8qp9_18545.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qp9_18545/08_2025/8qp9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qp9_18545/08_2025/8qp9_18545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qp9_18545/08_2025/8qp9_18545.map" model { file = "/net/cci-nas-00/data/ceres_data/8qp9_18545/08_2025/8qp9_18545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qp9_18545/08_2025/8qp9_18545.cif" } 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-2.0-5787/lib/python3.9/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: 5.90, per 1000 atoms: 0.23 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: 2.18 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 3.33 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: 7.53 Time building geometry restraints manager: 2.67 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: 36114 1.40 - 2.80: 523 2.80 - 4.20: 118 4.20 - 5.60: 34 5.60 - 7.00: 3 Bond angle restraints: 36792 Sorted by residual: angle pdb=" CA GLU C 375 " pdb=" C GLU C 375 " pdb=" N PRO C 376 " ideal model delta sigma weight residual 120.79 117.65 3.14 9.70e-01 1.06e+00 1.05e+01 angle pdb=" C3' G 5 57 " pdb=" O3' G 5 57 " pdb=" P U 5 58 " ideal model delta sigma weight residual 120.20 124.98 -4.78 1.50e+00 4.44e-01 1.02e+01 angle pdb=" C MET A1140 " pdb=" N ARG A1141 " pdb=" CA ARG A1141 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.83e+00 angle pdb=" C PRO A1417 " pdb=" N ARG A1418 " pdb=" CA ARG A1418 " ideal model delta sigma weight residual 121.54 126.58 -5.04 1.91e+00 2.74e-01 6.96e+00 angle pdb=" C ILE A1416 " pdb=" N PRO A1417 " pdb=" CA PRO A1417 " ideal model delta sigma weight residual 121.65 118.99 2.66 1.01e+00 9.80e-01 6.93e+00 ... (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: 6.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 28.160 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 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= 0.122 Angle : 0.476 7.002 36792 Z= 0.261 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 aren 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 covalent geometry : bond 0.00218 (25838) covalent geometry : angle 0.47551 (36792) hydrogen bonds : bond 0.18168 ( 1506) hydrogen bonds : angle 7.03644 ( 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 : 0.731 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.0972 time to fit residues: 22.7401 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 : 0.670 ------------------------------------------------------------------------------- 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: 10.0000 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: 10.0000 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.088568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.071928 restraints weight = 129600.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.071528 restraints weight = 179361.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.071258 restraints weight = 159459.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.070938 restraints weight = 141474.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.071080 restraints weight = 132992.739| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.100 25838 Z= 0.488 Angle : 0.954 18.066 36792 Z= 0.517 Chirality : 0.056 0.919 4852 Planarity : 0.007 0.071 4478 Dihedral : 17.531 178.446 6883 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.00 % Favored : 88.95 % Rotamer: Outliers : 0.95 % Allowed : 9.00 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -2.13 (0.13), residues: 3983 helix: -0.29 (0.12), residues: 1765 sheet: -2.63 (0.25), residues: 416 loop : -2.24 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 578 TYR 0.030 0.002 TYR C 198 PHE 0.045 0.003 PHE A1088 TRP 0.019 0.002 TRP A 637 HIS 0.013 0.004 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00910 (25838) covalent geometry : angle 0.95369 (36792) hydrogen bonds : bond 0.08136 ( 1506) hydrogen bonds : angle 6.59782 ( 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 116 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.557 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 116 average time/residue: 0.0977 time to fit residues: 21.4722 Evaluate side-chains 111 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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: 0.9990 chunk 224 optimal weight: 3.9990 chunk 310 optimal weight: 0.9990 chunk 303 optimal weight: 1.9990 chunk 362 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 273 optimal weight: 9.9990 chunk 312 optimal weight: 0.2980 chunk 14 optimal weight: 0.6980 chunk 344 optimal weight: 10.0000 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.092180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.075563 restraints weight = 128556.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.075344 restraints weight = 174861.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.074899 restraints weight = 143855.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.074657 restraints weight = 135372.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.074758 restraints weight = 126837.214| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 25838 Z= 0.113 Angle : 0.528 8.057 36792 Z= 0.271 Chirality : 0.041 0.222 4852 Planarity : 0.004 0.055 4478 Dihedral : 16.848 178.646 6883 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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 aren not related in a simple way. whole: -0.43 (0.14), residues: 3983 helix: 1.52 (0.13), residues: 1749 sheet: -2.25 (0.26), residues: 419 loop : -1.66 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 645 TYR 0.016 0.001 TYR C 327 PHE 0.014 0.001 PHE C 323 TRP 0.014 0.001 TRP C 344 HIS 0.001 0.000 HIS C 627 Details of bonding type rmsd covalent geometry : bond 0.00211 (25838) covalent geometry : angle 0.52765 (36792) hydrogen bonds : bond 0.04328 ( 1506) hydrogen bonds : angle 4.65070 ( 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 : 0.723 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1030 time to fit residues: 25.3442 Evaluate side-chains 120 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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: 30.0000 chunk 170 optimal weight: 0.6980 chunk 297 optimal weight: 5.9990 chunk 374 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 328 optimal weight: 9.9990 chunk 324 optimal weight: 0.5980 chunk 92 optimal weight: 20.0000 chunk 341 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.091524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.074865 restraints weight = 128053.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.074486 restraints weight = 178212.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.074326 restraints weight = 155219.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.074006 restraints weight = 136976.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.074121 restraints weight = 133542.402| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25838 Z= 0.141 Angle : 0.518 7.781 36792 Z= 0.268 Chirality : 0.041 0.219 4852 Planarity : 0.004 0.050 4478 Dihedral : 16.759 178.716 6883 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % 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 aren not related in a simple way. whole: -0.30 (0.14), residues: 3983 helix: 1.66 (0.13), residues: 1761 sheet: -2.23 (0.26), residues: 431 loop : -1.61 (0.16), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1139 TYR 0.012 0.001 TYR C 198 PHE 0.013 0.001 PHE A1088 TRP 0.010 0.001 TRP A 637 HIS 0.003 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00266 (25838) covalent geometry : angle 0.51811 (36792) hydrogen bonds : bond 0.04230 ( 1506) hydrogen bonds : angle 4.50558 ( 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 122 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.557 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0875 time to fit residues: 20.2953 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 : 0.740 ------------------------------------------------------------------------------- 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: 10.0000 chunk 410 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 256 optimal weight: 9.9990 chunk 141 optimal weight: 0.9990 chunk 199 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 224 optimal weight: 7.9990 chunk 407 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3682 r_free = 0.3682 target = 0.091237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.074704 restraints weight = 127312.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.074188 restraints weight = 188347.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.074438 restraints weight = 175100.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.073990 restraints weight = 143733.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.074134 restraints weight = 142546.059| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25838 Z= 0.156 Angle : 0.530 7.730 36792 Z= 0.277 Chirality : 0.042 0.223 4852 Planarity : 0.004 0.053 4478 Dihedral : 16.841 178.416 6883 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.14), residues: 3983 helix: 1.56 (0.13), residues: 1763 sheet: -2.31 (0.25), residues: 428 loop : -1.63 (0.16), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1139 TYR 0.014 0.001 TYR C 275 PHE 0.015 0.001 PHE A1088 TRP 0.012 0.001 TRP A 637 HIS 0.005 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00294 (25838) covalent geometry : angle 0.52967 (36792) hydrogen bonds : bond 0.04255 ( 1506) hydrogen bonds : angle 4.55990 ( 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 : 0.762 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0949 time to fit residues: 22.2261 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 : 0.798 ------------------------------------------------------------------------------- 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: 20.0000 chunk 312 optimal weight: 0.0010 chunk 50 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 55 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 259 optimal weight: 0.4980 chunk 354 optimal weight: 0.0040 chunk 288 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.092790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.076259 restraints weight = 128975.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.076006 restraints weight = 164004.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.075051 restraints weight = 134475.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.075124 restraints weight = 145062.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.075153 restraints weight = 121244.678| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25838 Z= 0.086 Angle : 0.467 7.811 36792 Z= 0.235 Chirality : 0.040 0.211 4852 Planarity : 0.004 0.049 4478 Dihedral : 16.570 179.707 6883 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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 aren not related in a simple way. whole: 0.26 (0.14), residues: 3983 helix: 2.22 (0.13), residues: 1767 sheet: -2.13 (0.26), residues: 441 loop : -1.38 (0.16), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1141 TYR 0.015 0.001 TYR C 327 PHE 0.018 0.001 PHE C 323 TRP 0.009 0.001 TRP C 531 HIS 0.004 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00167 (25838) covalent geometry : angle 0.46670 (36792) hydrogen bonds : bond 0.03455 ( 1506) hydrogen bonds : angle 3.85120 ( 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 128 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.661 Fit side-chains REVERT: C 138 LEU cc_start: 0.8370 (tp) cc_final: 0.8120 (tt) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.0912 time to fit residues: 22.4668 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 : 0.723 ------------------------------------------------------------------------------- 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: 2.9990 chunk 71 optimal weight: 20.0000 chunk 212 optimal weight: 3.9990 chunk 317 optimal weight: 0.0270 chunk 22 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 345 optimal weight: 0.9990 chunk 255 optimal weight: 0.6980 chunk 175 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 376 optimal weight: 20.0000 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.091940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.075500 restraints weight = 129054.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.075329 restraints weight = 167722.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.074082 restraints weight = 124478.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.073921 restraints weight = 148772.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.073997 restraints weight = 146975.313| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.1607 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= 0.119 Angle : 0.481 7.674 36792 Z= 0.246 Chirality : 0.040 0.233 4852 Planarity : 0.004 0.049 4478 Dihedral : 16.607 178.944 6883 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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 aren not related in a simple way. whole: 0.24 (0.14), residues: 3983 helix: 2.16 (0.13), residues: 1766 sheet: -2.13 (0.26), residues: 436 loop : -1.36 (0.16), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1141 TYR 0.010 0.001 TYR C 275 PHE 0.010 0.001 PHE C 323 TRP 0.010 0.001 TRP A 637 HIS 0.006 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00228 (25838) covalent geometry : angle 0.48146 (36792) hydrogen bonds : bond 0.03658 ( 1506) hydrogen bonds : angle 3.98605 ( 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 125 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.557 Fit side-chains REVERT: C 138 LEU cc_start: 0.8410 (tp) cc_final: 0.8075 (tt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0913 time to fit residues: 21.7010 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 : 1.371 ------------------------------------------------------------------------------- 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: 9.9990 chunk 54 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 234 optimal weight: 1.9990 chunk 244 optimal weight: 0.0470 chunk 321 optimal weight: 20.0000 chunk 117 optimal weight: 30.0000 chunk 199 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.090465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.073875 restraints weight = 128292.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.073575 restraints weight = 193385.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.073100 restraints weight = 160372.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.072787 restraints weight = 156288.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.072921 restraints weight = 152238.215| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 25838 Z= 0.247 Angle : 0.612 8.538 36792 Z= 0.330 Chirality : 0.044 0.258 4852 Planarity : 0.005 0.054 4478 Dihedral : 16.998 177.272 6883 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % 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 aren not related in a simple way. whole: -0.59 (0.14), residues: 3983 helix: 1.33 (0.12), residues: 1752 sheet: -2.37 (0.25), residues: 441 loop : -1.64 (0.15), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1139 TYR 0.040 0.002 TYR C 378 PHE 0.037 0.002 PHE C 228 TRP 0.013 0.001 TRP A 637 HIS 0.009 0.002 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00465 (25838) covalent geometry : angle 0.61229 (36792) hydrogen bonds : bond 0.04774 ( 1506) hydrogen bonds : angle 4.88744 ( 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 121 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.714 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0882 time to fit residues: 20.9239 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 : 0.688 ------------------------------------------------------------------------------- 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: 6.9990 chunk 385 optimal weight: 2.9990 chunk 282 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 367 optimal weight: 5.9990 chunk 371 optimal weight: 3.9990 chunk 294 optimal weight: 9.9990 chunk 386 optimal weight: 0.0270 chunk 93 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 261 optimal weight: 10.0000 overall best weight: 1.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.091620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.075027 restraints weight = 127863.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.074588 restraints weight = 174716.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.074575 restraints weight = 166276.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.074255 restraints weight = 143424.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.074406 restraints weight = 132436.852| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25838 Z= 0.130 Angle : 0.503 7.583 36792 Z= 0.260 Chirality : 0.041 0.227 4852 Planarity : 0.004 0.051 4478 Dihedral : 16.817 178.879 6883 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % 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 aren not related in a simple way. whole: -0.10 (0.14), residues: 3983 helix: 1.82 (0.13), residues: 1761 sheet: -2.16 (0.26), residues: 411 loop : -1.51 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 645 TYR 0.018 0.001 TYR C 327 PHE 0.018 0.001 PHE C 228 TRP 0.010 0.001 TRP A 637 HIS 0.007 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00248 (25838) covalent geometry : angle 0.50285 (36792) hydrogen bonds : bond 0.03815 ( 1506) hydrogen bonds : angle 4.30773 ( 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 122 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.699 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0909 time to fit residues: 21.3753 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 : 0.778 ------------------------------------------------------------------------------- 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: 0.7980 chunk 52 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 340 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 396 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 271 optimal weight: 0.0070 chunk 385 optimal weight: 0.8980 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.092069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.075597 restraints weight = 128563.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.075207 restraints weight = 178111.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.074863 restraints weight = 145656.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.074558 restraints weight = 144363.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.074741 restraints weight = 128783.295| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.1735 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= 0.098 Angle : 0.471 7.572 36792 Z= 0.240 Chirality : 0.040 0.217 4852 Planarity : 0.004 0.050 4478 Dihedral : 16.675 179.896 6883 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % 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 aren not related in a simple way. whole: 0.21 (0.14), residues: 3983 helix: 2.13 (0.13), residues: 1767 sheet: -2.15 (0.26), residues: 418 loop : -1.37 (0.16), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1139 TYR 0.016 0.001 TYR C 327 PHE 0.015 0.001 PHE C 228 TRP 0.009 0.000 TRP A 637 HIS 0.006 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00190 (25838) covalent geometry : angle 0.47105 (36792) hydrogen bonds : bond 0.03514 ( 1506) hydrogen bonds : angle 3.97446 ( 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 : 0.572 Fit side-chains REVERT: C 138 LEU cc_start: 0.8406 (tp) cc_final: 0.8092 (tt) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0993 time to fit residues: 22.9911 Evaluate side-chains 120 residues out of total 3622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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: 0.2980 chunk 373 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 213 optimal weight: 0.9990 chunk 165 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 278 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.092871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.076405 restraints weight = 128446.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.076100 restraints weight = 178920.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.075704 restraints weight = 149125.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.075448 restraints weight = 136402.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.075562 restraints weight = 132718.141| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25838 Z= 0.085 Angle : 0.452 7.670 36792 Z= 0.227 Chirality : 0.039 0.220 4852 Planarity : 0.004 0.051 4478 Dihedral : 16.533 179.934 6883 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % 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 aren not related in a simple way. whole: 0.54 (0.15), residues: 3983 helix: 2.42 (0.13), residues: 1769 sheet: -1.97 (0.26), residues: 437 loop : -1.22 (0.16), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1139 TYR 0.015 0.001 TYR C 327 PHE 0.008 0.001 PHE C 228 TRP 0.006 0.000 TRP A 637 HIS 0.004 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00169 (25838) covalent geometry : angle 0.45230 (36792) hydrogen bonds : bond 0.03248 ( 1506) hydrogen bonds : angle 3.64442 ( 4227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2763.40 seconds wall clock time: 48 minutes 17.15 seconds (2897.15 seconds total)