Starting phenix.real_space_refine on Wed Jul 24 04:36:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qp9_18545/07_2024/8qp9_18545.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qp9_18545/07_2024/8qp9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qp9_18545/07_2024/8qp9_18545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qp9_18545/07_2024/8qp9_18545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qp9_18545/07_2024/8qp9_18545.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qp9_18545/07_2024/8qp9_18545.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} 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: {'GLN:plan1': 7, 'ASP:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 7} 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: {'GLN:plan1': 26, 'HIS:plan': 13, 'TYR:plan': 13, 'ASN:plan1': 22, 'TRP:plan': 6, 'ASP:plan': 57, 'PHE:plan': 21, 'GLU:plan': 57, 'ARG:plan': 31} 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: {'GLN:plan1': 3, 'ARG:plan': 7, 'TYR:plan': 8, 'ASN:plan1': 8, 'TRP:plan': 3, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 9, 'HIS: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, 'ARG:plan': 5, 'GLN:plan1': 4} 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: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 8} 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: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 7, 'GLU:plan': 5, 'ARG:plan': 11} 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: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5} 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: {'GLN:plan1': 21, 'HIS:plan': 17, 'TYR:plan': 23, 'ASN:plan1': 27, 'TRP:plan': 4, 'ASP:plan': 23, 'PHE:plan': 26, 'GLU:plan': 25, 'ARG:plan': 18} 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, 'GLN:plan1': 2, 'ASN:plan1': 3, 'PHE:plan': 1, 'ARG:plan': 4} 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: {'GLN:plan1': 7, 'ASP:plan': 8, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 13} 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: {'GLN:plan1': 82, 'ASP:plan': 111, 'TYR:plan': 82, 'ASN:plan1': 100, 'TRP:plan': 49, 'HIS:plan': 56, 'PHE:plan': 81, 'GLU:plan': 111, 'ARG:plan': 125} 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: {'GLN:plan1': 7, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 4, 'GLU:plan': 18, 'ARG:plan': 13} 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: 16.17, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.86 Conformation dependent library (CDL) restraints added in 5.4 seconds 7966 Ramachandran restraints generated. 3983 Oldfield, 0 Emsley, 3983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7654 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 34 sheets defined 46.9% alpha, 8.9% beta 49 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 10.70 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: 17.05 Time building geometry restraints manager: 12.75 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: 100.57 - 107.26: 1967 107.26 - 113.95: 14816 113.95 - 120.65: 10052 120.65 - 127.34: 9447 127.34 - 134.03: 510 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 2.440 nonbonded pdb=" O HIS C 451 " pdb=" NH1 ARG C 578 " model vdw 2.250 2.520 nonbonded pdb=" O SER C 183 " pdb=" OH TYR C 482 " model vdw 2.252 2.440 nonbonded pdb=" N2 G 5 8 " pdb=" O2 U 5 74 " model vdw 2.293 2.520 nonbonded pdb=" N6 A 6 69 " pdb=" O4 U 4 5 " model vdw 2.297 2.520 ... (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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.280 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: 0.030 Extract box with map and model: 1.050 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 87.840 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.100 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.950 ------------------------------------------------------------------------------- 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= 0.150 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (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 TRP 0.014 0.001 TRP C 531 HIS 0.001 0.000 HIS C 139 PHE 0.011 0.001 PHE C 323 TYR 0.021 0.001 TYR C 327 ARG 0.005 0.001 ARG C 529 *********************** 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 fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.578 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2534 time to fit residues: 61.6235 Evaluate side-chains 118 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 349 optimal weight: 6.9990 chunk 313 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 167 optimal weight: 30.0000 chunk 324 optimal weight: 0.6980 chunk 125 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 241 optimal weight: 0.7980 chunk 375 optimal weight: 20.0000 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25838 Z= 0.345 Angle : 0.700 18.511 36792 Z= 0.360 Chirality : 0.047 0.652 4852 Planarity : 0.005 0.053 4478 Dihedral : 17.025 178.944 6883 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.36 % Favored : 91.61 % Rotamer: Outliers : 0.71 % Allowed : 4.50 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3983 helix: 1.09 (0.12), residues: 1759 sheet: -2.19 (0.26), residues: 422 loop : -1.72 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 637 HIS 0.007 0.002 HIS C 245 PHE 0.029 0.002 PHE A 387 TYR 0.020 0.002 TYR C 198 ARG 0.005 0.001 ARG C 645 *********************** 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 122 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 2.561 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 122 average time/residue: 0.2327 time to fit residues: 56.1429 Evaluate side-chains 115 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 208 optimal weight: 0.0870 chunk 116 optimal weight: 30.0000 chunk 312 optimal weight: 7.9990 chunk 256 optimal weight: 9.9990 chunk 103 optimal weight: 0.0980 chunk 376 optimal weight: 30.0000 chunk 406 optimal weight: 0.4980 chunk 335 optimal weight: 4.9990 chunk 373 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 302 optimal weight: 0.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25838 Z= 0.134 Angle : 0.493 7.863 36792 Z= 0.250 Chirality : 0.040 0.262 4852 Planarity : 0.004 0.047 4478 Dihedral : 16.728 179.897 6883 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3983 helix: 1.85 (0.13), residues: 1765 sheet: -1.98 (0.26), residues: 428 loop : -1.47 (0.16), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 637 HIS 0.002 0.000 HIS C 627 PHE 0.012 0.001 PHE C 323 TYR 0.016 0.001 TYR C 327 ARG 0.001 0.000 ARG C 578 *********************** 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 128 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.613 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2637 time to fit residues: 64.4161 Evaluate side-chains 116 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 372 optimal weight: 6.9990 chunk 283 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 179 optimal weight: 0.5980 chunk 252 optimal weight: 5.9990 chunk 377 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 358 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25838 Z= 0.262 Angle : 0.567 7.766 36792 Z= 0.300 Chirality : 0.043 0.215 4852 Planarity : 0.005 0.049 4478 Dihedral : 16.887 179.824 6883 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3983 helix: 1.45 (0.13), residues: 1751 sheet: -2.15 (0.26), residues: 425 loop : -1.62 (0.16), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 637 HIS 0.006 0.002 HIS C 245 PHE 0.019 0.001 PHE C 323 TYR 0.016 0.001 TYR C 275 ARG 0.003 0.001 ARG C 177 *********************** 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 123 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.627 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2527 time to fit residues: 60.5828 Evaluate side-chains 113 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 333 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 341 optimal weight: 5.9990 chunk 276 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 204 optimal weight: 20.0000 chunk 359 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25838 Z= 0.214 Angle : 0.534 8.046 36792 Z= 0.279 Chirality : 0.042 0.232 4852 Planarity : 0.004 0.048 4478 Dihedral : 16.871 179.835 6883 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3983 helix: 1.58 (0.13), residues: 1743 sheet: -2.18 (0.26), residues: 425 loop : -1.63 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 637 HIS 0.005 0.001 HIS C 245 PHE 0.025 0.001 PHE C 228 TYR 0.015 0.001 TYR C 275 ARG 0.002 0.000 ARG C 177 *********************** 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 122 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 2.581 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2462 time to fit residues: 59.0078 Evaluate side-chains 115 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 134 optimal weight: 0.7980 chunk 360 optimal weight: 6.9990 chunk 79 optimal weight: 0.0870 chunk 234 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 400 optimal weight: 30.0000 chunk 332 optimal weight: 4.9990 chunk 185 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 210 optimal weight: 6.9990 overall best weight: 1.9960 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25838 Z= 0.168 Angle : 0.499 7.776 36792 Z= 0.257 Chirality : 0.041 0.209 4852 Planarity : 0.004 0.047 4478 Dihedral : 16.790 179.663 6883 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3983 helix: 1.80 (0.13), residues: 1758 sheet: -2.19 (0.26), residues: 425 loop : -1.51 (0.16), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 637 HIS 0.003 0.001 HIS C 245 PHE 0.020 0.001 PHE C 228 TYR 0.011 0.001 TYR C 198 ARG 0.001 0.000 ARG A1141 *********************** 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 126 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 2.489 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2604 time to fit residues: 63.8326 Evaluate side-chains 117 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 386 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 chunk 292 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 337 optimal weight: 5.9990 chunk 223 optimal weight: 8.9990 chunk 399 optimal weight: 4.9990 chunk 249 optimal weight: 20.0000 chunk 243 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25838 Z= 0.268 Angle : 0.575 8.763 36792 Z= 0.305 Chirality : 0.043 0.245 4852 Planarity : 0.005 0.052 4478 Dihedral : 16.974 179.727 6883 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3983 helix: 1.35 (0.12), residues: 1754 sheet: -2.26 (0.26), residues: 425 loop : -1.70 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 637 HIS 0.005 0.001 HIS C 137 PHE 0.029 0.001 PHE C 228 TYR 0.018 0.001 TYR C 275 ARG 0.003 0.001 ARG C 177 *********************** 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 122 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 2.826 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2511 time to fit residues: 59.6862 Evaluate side-chains 114 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 246 optimal weight: 4.9990 chunk 159 optimal weight: 0.2980 chunk 238 optimal weight: 20.0000 chunk 120 optimal weight: 40.0000 chunk 78 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 253 optimal weight: 8.9990 chunk 271 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 313 optimal weight: 10.0000 overall best weight: 3.8588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25838 Z= 0.276 Angle : 0.589 10.688 36792 Z= 0.314 Chirality : 0.043 0.255 4852 Planarity : 0.005 0.055 4478 Dihedral : 17.079 178.676 6883 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3983 helix: 1.16 (0.12), residues: 1746 sheet: -2.54 (0.25), residues: 431 loop : -1.76 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 531 HIS 0.007 0.002 HIS C 245 PHE 0.027 0.001 PHE C 228 TYR 0.021 0.001 TYR A1019 ARG 0.004 0.001 ARG C 645 *********************** 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 120 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 3.389 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2471 time to fit residues: 58.4800 Evaluate side-chains 114 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 362 optimal weight: 4.9990 chunk 382 optimal weight: 20.0000 chunk 348 optimal weight: 20.0000 chunk 371 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 161 optimal weight: 30.0000 chunk 291 optimal weight: 0.6980 chunk 114 optimal weight: 0.0980 chunk 336 optimal weight: 8.9990 chunk 351 optimal weight: 8.9990 chunk 370 optimal weight: 0.9980 overall best weight: 3.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25838 Z= 0.238 Angle : 0.560 10.555 36792 Z= 0.295 Chirality : 0.042 0.237 4852 Planarity : 0.005 0.055 4478 Dihedral : 17.019 178.791 6883 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3983 helix: 1.35 (0.13), residues: 1737 sheet: -2.50 (0.25), residues: 430 loop : -1.73 (0.15), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 637 HIS 0.005 0.001 HIS C 245 PHE 0.021 0.001 PHE C 228 TYR 0.016 0.001 TYR C 275 ARG 0.003 0.001 ARG C 578 *********************** 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 fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 2.521 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2924 time to fit residues: 70.8924 Evaluate side-chains 115 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 244 optimal weight: 1.9990 chunk 393 optimal weight: 0.7980 chunk 239 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 273 optimal weight: 7.9990 chunk 412 optimal weight: 20.0000 chunk 379 optimal weight: 40.0000 chunk 328 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 253 optimal weight: 8.9990 chunk 201 optimal weight: 30.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25838 Z= 0.250 Angle : 0.571 10.894 36792 Z= 0.302 Chirality : 0.043 0.248 4852 Planarity : 0.005 0.055 4478 Dihedral : 17.058 178.113 6883 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3983 helix: 1.28 (0.12), residues: 1744 sheet: -2.58 (0.25), residues: 440 loop : -1.75 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 637 HIS 0.006 0.002 HIS C 245 PHE 0.022 0.001 PHE C 323 TYR 0.037 0.001 TYR C 327 ARG 0.003 0.001 ARG C 578 ********************** 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 121 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.480 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.2458 time to fit residues: 58.4763 Evaluate side-chains 114 residues out of total 3622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 260 optimal weight: 2.9990 chunk 349 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 chunk 302 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 328 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 337 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.091395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.074982 restraints weight = 127853.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.074526 restraints weight = 173819.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.074274 restraints weight = 159376.500| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25838 Z= 0.175 Angle : 0.514 9.736 36792 Z= 0.265 Chirality : 0.041 0.219 4852 Planarity : 0.004 0.053 4478 Dihedral : 16.901 179.840 6883 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3983 helix: 1.69 (0.13), residues: 1748 sheet: -2.34 (0.26), residues: 439 loop : -1.60 (0.16), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 637 HIS 0.003 0.001 HIS C 245 PHE 0.018 0.001 PHE C 323 TYR 0.020 0.001 TYR C 378 ARG 0.002 0.001 ARG C 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3487.65 seconds wall clock time: 62 minutes 49.56 seconds (3769.56 seconds total)