Starting phenix.real_space_refine on Wed Mar 4 17:58:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d33_27154/03_2026/8d33_27154.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d33_27154/03_2026/8d33_27154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d33_27154/03_2026/8d33_27154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d33_27154/03_2026/8d33_27154.map" model { file = "/net/cci-nas-00/data/ceres_data/8d33_27154/03_2026/8d33_27154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d33_27154/03_2026/8d33_27154.cif" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.325 sd= 0.631 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 49 5.49 5 S 82 5.16 5 C 9585 2.51 5 N 2683 2.21 5 O 2872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15272 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7778 Classifications: {'peptide': 974} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 65, 'TRANS': 908} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3307 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3213 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "T" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 494 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' CA': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.46, per 1000 atoms: 0.23 Number of scatterers: 15272 At special positions: 0 Unit cell: (107.1, 124.95, 153, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 82 16.00 P 49 15.00 O 2872 8.00 N 2683 7.00 C 9585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A1077 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.48 Conformation dependent library (CDL) restraints added in 593.2 milliseconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3322 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 12 sheets defined 48.3% alpha, 14.1% beta 22 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 203 through 206 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 277 through 283 removed outlier: 6.860A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.115A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 472 removed outlier: 3.523A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 482 removed outlier: 5.242A pdb=" N GLY A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 478 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TYR A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 554 removed outlier: 3.835A pdb=" N GLN A 541 " --> pdb=" O GLU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.677A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 604 Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 786 through 810 removed outlier: 5.079A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 923 removed outlier: 3.712A pdb=" N GLN A 922 " --> pdb=" O TRP A 918 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 923 " --> pdb=" O MET A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 940 Processing helix chain 'A' and resid 942 through 955 Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 974 through 987 removed outlier: 3.750A pdb=" N MET A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1067 Processing helix chain 'A' and resid 1080 through 1084 removed outlier: 3.616A pdb=" N GLU A1084 " --> pdb=" O ARG A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.572A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1167 Processing helix chain 'A' and resid 1174 through 1178 removed outlier: 3.589A pdb=" N VAL A1177 " --> pdb=" O PRO A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1228 Processing helix chain 'B' and resid 65 through 76 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 165 through 178 removed outlier: 3.877A pdb=" N ALA B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 192 through 193 No H-bonds generated for 'chain 'B' and resid 192 through 193' Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.580A pdb=" N ASP B 198 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 266 removed outlier: 3.784A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 318 through 323 removed outlier: 3.500A pdb=" N LYS B 321 " --> pdb=" O ASN B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.638A pdb=" N PHE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN B 355 " --> pdb=" O TYR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 391 through 409 removed outlier: 3.657A pdb=" N ASN B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 444 through 451 removed outlier: 3.508A pdb=" N LEU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 483 removed outlier: 4.492A pdb=" N LYS B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ASP B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 150 through 155 Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 166 through 178 removed outlier: 3.638A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 191 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.110A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 391 through 409 Processing helix chain 'C' and resid 417 through 420 removed outlier: 3.566A pdb=" N THR C 420 " --> pdb=" O TYR C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.718A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 450 " --> pdb=" O THR C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 485 removed outlier: 4.610A pdb=" N LYS C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.910A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA A 212 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA A 214 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 196 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N SER A 216 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N ALA A 194 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 438 Processing sheet with id=AA3, first strand: chain 'A' and resid 747 through 751 Processing sheet with id=AA4, first strand: chain 'A' and resid 1127 through 1132 removed outlier: 6.688A pdb=" N ARG A1138 " --> pdb=" O CYS A1130 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER A1132 " --> pdb=" O GLU A1136 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU A1136 " --> pdb=" O SER A1132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.379A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL B 335 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LYS B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 148 removed outlier: 4.037A pdb=" N GLY C 179 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS C 180 " --> pdb=" O LYS C 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA9, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.405A pdb=" N TRP B 414 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS B 382 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL B 441 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 127 removed outlier: 6.182A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ILE C 211 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU C 301 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB3, first strand: chain 'C' and resid 413 through 415 removed outlier: 6.176A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1887 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 112 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4795 1.34 - 1.46: 3021 1.46 - 1.58: 7714 1.58 - 1.70: 91 1.70 - 1.82: 130 Bond restraints: 15751 Sorted by residual: bond pdb=" O5' DCP A1302 " pdb=" PA DCP A1302 " ideal model delta sigma weight residual 1.579 1.805 -0.226 1.50e-02 4.44e+03 2.28e+02 bond pdb=" C5' DCP A1302 " pdb=" O5' DCP A1302 " ideal model delta sigma weight residual 1.443 1.323 0.120 1.10e-02 8.26e+03 1.19e+02 bond pdb=" O3A DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 1.592 1.707 -0.115 1.10e-02 8.26e+03 1.09e+02 bond pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 1.600 1.650 -0.050 1.10e-02 8.26e+03 2.10e+01 bond pdb=" C4 DCP A1302 " pdb=" N4 DCP A1302 " ideal model delta sigma weight residual 1.334 1.389 -0.055 1.20e-02 6.94e+03 2.06e+01 ... (remaining 15746 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 21483 3.38 - 6.76: 54 6.76 - 10.14: 6 10.14 - 13.52: 2 13.52 - 16.90: 2 Bond angle restraints: 21547 Sorted by residual: angle pdb=" O2B DCP A1302 " pdb=" PB DCP A1302 " pdb=" O3B DCP A1302 " ideal model delta sigma weight residual 106.94 123.84 -16.90 1.88e+00 2.83e-01 8.08e+01 angle pdb=" O2A DCP A1302 " pdb=" PA DCP A1302 " pdb=" O3A DCP A1302 " ideal model delta sigma weight residual 106.94 123.75 -16.81 1.88e+00 2.83e-01 8.00e+01 angle pdb=" PB DCP A1302 " pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 139.87 132.92 6.95 1.00e+00 1.00e+00 4.83e+01 angle pdb=" O2G DCP A1302 " pdb=" PG DCP A1302 " pdb=" O3B DCP A1302 " ideal model delta sigma weight residual 104.48 97.94 6.54 1.14e+00 7.76e-01 3.32e+01 angle pdb=" C1' DCP A1302 " pdb=" N1 DCP A1302 " pdb=" C6 DCP A1302 " ideal model delta sigma weight residual 121.66 114.58 7.08 1.39e+00 5.21e-01 2.61e+01 ... (remaining 21542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8613 17.84 - 35.68: 483 35.68 - 53.52: 148 53.52 - 71.36: 35 71.36 - 89.20: 13 Dihedral angle restraints: 9292 sinusoidal: 4145 harmonic: 5147 Sorted by residual: dihedral pdb=" CB CYS A 418 " pdb=" SG CYS A 418 " pdb=" SG CYS A1077 " pdb=" CB CYS A1077 " ideal model delta sinusoidal sigma weight residual 93.00 130.66 -37.66 1 1.00e+01 1.00e-02 2.00e+01 dihedral pdb=" CA LEU A 195 " pdb=" C LEU A 195 " pdb=" N VAL A 196 " pdb=" CA VAL A 196 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLU A 181 " pdb=" C GLU A 181 " pdb=" N GLY A 182 " pdb=" CA GLY A 182 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 9289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1558 0.030 - 0.060: 505 0.060 - 0.089: 141 0.089 - 0.119: 97 0.119 - 0.149: 21 Chirality restraints: 2322 Sorted by residual: chirality pdb=" C4' DCP A1302 " pdb=" C3' DCP A1302 " pdb=" C5' DCP A1302 " pdb=" O4' DCP A1302 " both_signs ideal model delta sigma weight residual False -2.50 -2.65 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA ILE A 744 " pdb=" N ILE A 744 " pdb=" C ILE A 744 " pdb=" CB ILE A 744 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA VAL B 332 " pdb=" N VAL B 332 " pdb=" C VAL B 332 " pdb=" CB VAL B 332 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 2319 not shown) Planarity restraints: 2602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 452 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.55e+00 pdb=" C TYR A 452 " 0.022 2.00e-02 2.50e+03 pdb=" O TYR A 452 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU A 453 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC T 21 " -0.015 2.00e-02 2.50e+03 7.52e-03 1.27e+00 pdb=" N1 DC T 21 " 0.016 2.00e-02 2.50e+03 pdb=" C2 DC T 21 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC T 21 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DC T 21 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DC T 21 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC T 21 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC T 21 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC T 21 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 482 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.18e+00 pdb=" N PRO A 483 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 483 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 483 " 0.015 5.00e-02 4.00e+02 ... (remaining 2599 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 200 2.65 - 3.21: 13847 3.21 - 3.78: 23198 3.78 - 4.34: 32745 4.34 - 4.90: 52114 Nonbonded interactions: 122104 Sorted by model distance: nonbonded pdb=" OE2 GLU B 165 " pdb=" NZ LYS C 160 " model vdw 2.091 3.120 nonbonded pdb=" O THR B 460 " pdb=" OG1 THR B 461 " model vdw 2.095 3.040 nonbonded pdb=" OG SER A1230 " pdb=" OE1 GLU A1232 " model vdw 2.105 3.040 nonbonded pdb=" O PRO A 217 " pdb=" OG SER A 218 " model vdw 2.125 3.040 nonbonded pdb=" O THR C 460 " pdb=" OG1 THR C 461 " model vdw 2.130 3.040 ... (remaining 122099 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 67 through 218 or (resid 219 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 228 and (name N or name CA or name C or na \ me O or name CB )) or resid 229 through 355 or resid 368 through 485)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.760 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.226 15752 Z= 0.216 Angle : 0.546 16.903 21549 Z= 0.306 Chirality : 0.038 0.149 2322 Planarity : 0.003 0.027 2602 Dihedral : 13.188 89.196 5967 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 0.39 % Allowed : 4.39 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.21), residues: 1758 helix: 1.34 (0.20), residues: 739 sheet: 0.94 (0.31), residues: 242 loop : -0.16 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 574 TYR 0.009 0.001 TYR A1108 PHE 0.014 0.001 PHE A 197 TRP 0.006 0.001 TRP A 220 HIS 0.002 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00330 (15751) covalent geometry : angle 0.54555 (21547) SS BOND : bond 0.00604 ( 1) SS BOND : angle 0.99494 ( 2) hydrogen bonds : bond 0.15236 ( 733) hydrogen bonds : angle 6.12378 ( 1999) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 488 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 VAL cc_start: 0.8762 (p) cc_final: 0.8499 (t) REVERT: A 877 MET cc_start: 0.7530 (mmm) cc_final: 0.7325 (mmt) REVERT: A 993 ARG cc_start: 0.6388 (tpp-160) cc_final: 0.6020 (tpm-80) REVERT: A 1095 SER cc_start: 0.7752 (m) cc_final: 0.7529 (t) REVERT: B 257 ARG cc_start: 0.7323 (mtp-110) cc_final: 0.6973 (mtp-110) REVERT: B 310 GLU cc_start: 0.7841 (mp0) cc_final: 0.7493 (mp0) REVERT: B 462 MET cc_start: 0.8512 (mmm) cc_final: 0.8263 (mmm) REVERT: C 129 ASP cc_start: 0.7081 (t70) cc_final: 0.6837 (t0) REVERT: C 455 LEU cc_start: 0.8316 (tt) cc_final: 0.8090 (tp) outliers start: 6 outliers final: 1 residues processed: 492 average time/residue: 0.6348 time to fit residues: 340.6161 Evaluate side-chains 386 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 385 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 258 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1098 ASN A1157 ASN A1175 GLN B 195 ASN B 323 HIS B 339 ASN B 409 ASN C 166 GLN C 339 ASN C 400 GLN C 409 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.121499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.113238 restraints weight = 26032.007| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.38 r_work: 0.3539 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 15752 Z= 0.287 Angle : 0.764 9.726 21549 Z= 0.405 Chirality : 0.050 0.200 2322 Planarity : 0.007 0.067 2602 Dihedral : 14.393 85.311 2460 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.38 % Favored : 95.56 % Rotamer: Outliers : 4.39 % Allowed : 15.12 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.19), residues: 1758 helix: 1.07 (0.19), residues: 744 sheet: 0.97 (0.31), residues: 233 loop : -0.52 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 279 TYR 0.022 0.003 TYR A 649 PHE 0.034 0.003 PHE A 197 TRP 0.013 0.002 TRP A 607 HIS 0.005 0.002 HIS A 733 Details of bonding type rmsd covalent geometry : bond 0.00653 (15751) covalent geometry : angle 0.76386 (21547) SS BOND : bond 0.00871 ( 1) SS BOND : angle 1.02270 ( 2) hydrogen bonds : bond 0.07013 ( 733) hydrogen bonds : angle 5.01851 ( 1999) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 358 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 543 VAL cc_start: 0.8690 (p) cc_final: 0.8431 (t) REVERT: A 546 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8226 (ttm170) REVERT: A 877 MET cc_start: 0.7534 (mmm) cc_final: 0.7316 (mmt) REVERT: A 993 ARG cc_start: 0.6364 (tpp-160) cc_final: 0.6004 (tpm-80) REVERT: A 1102 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: B 134 LYS cc_start: 0.8397 (tptp) cc_final: 0.8138 (tttm) REVERT: B 310 GLU cc_start: 0.8000 (mp0) cc_final: 0.7606 (mp0) REVERT: B 462 MET cc_start: 0.8497 (mmm) cc_final: 0.8279 (mmm) REVERT: C 86 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6571 (mm) outliers start: 68 outliers final: 37 residues processed: 395 average time/residue: 0.6117 time to fit residues: 264.5493 Evaluate side-chains 378 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 338 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1102 GLN Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 430 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 82 optimal weight: 0.0020 chunk 38 optimal weight: 5.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS A 115 GLN A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1175 GLN B 195 ASN B 261 GLN C 339 ASN C 400 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.123655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.115282 restraints weight = 26150.762| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.41 r_work: 0.3569 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15752 Z= 0.159 Angle : 0.620 8.796 21549 Z= 0.329 Chirality : 0.043 0.163 2322 Planarity : 0.005 0.042 2602 Dihedral : 14.332 83.837 2460 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.99 % Rotamer: Outliers : 3.62 % Allowed : 17.83 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1758 helix: 1.45 (0.19), residues: 744 sheet: 1.11 (0.32), residues: 227 loop : -0.41 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 657 TYR 0.016 0.002 TYR A 150 PHE 0.025 0.002 PHE A 197 TRP 0.013 0.001 TRP A 897 HIS 0.003 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00354 (15751) covalent geometry : angle 0.62050 (21547) SS BOND : bond 0.00487 ( 1) SS BOND : angle 0.60103 ( 2) hydrogen bonds : bond 0.05243 ( 733) hydrogen bonds : angle 4.69036 ( 1999) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 366 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 543 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8374 (t) REVERT: A 877 MET cc_start: 0.7516 (mmm) cc_final: 0.7294 (mmt) REVERT: B 134 LYS cc_start: 0.8381 (tptp) cc_final: 0.8137 (tttp) REVERT: B 310 GLU cc_start: 0.7933 (mp0) cc_final: 0.7471 (mp0) REVERT: B 462 MET cc_start: 0.8477 (mmm) cc_final: 0.8254 (mmm) REVERT: C 86 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6596 (mm) outliers start: 56 outliers final: 31 residues processed: 401 average time/residue: 0.6218 time to fit residues: 272.8891 Evaluate side-chains 374 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 341 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 453 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 157 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 238 GLN A 270 ASN A 468 ASN A 564 GLN A 736 ASN A 843 GLN A1175 GLN B 195 ASN B 261 GLN B 305 ASN C 339 ASN C 400 GLN C 409 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.122789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.114484 restraints weight = 26151.878| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.40 r_work: 0.3560 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15752 Z= 0.191 Angle : 0.653 9.080 21549 Z= 0.345 Chirality : 0.044 0.162 2322 Planarity : 0.006 0.046 2602 Dihedral : 14.418 86.153 2460 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.36 % Rotamer: Outliers : 4.97 % Allowed : 17.64 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.20), residues: 1758 helix: 1.31 (0.19), residues: 750 sheet: 1.04 (0.30), residues: 242 loop : -0.43 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 361 TYR 0.017 0.002 TYR A 150 PHE 0.025 0.002 PHE A 197 TRP 0.013 0.002 TRP A 175 HIS 0.004 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00433 (15751) covalent geometry : angle 0.65321 (21547) SS BOND : bond 0.00570 ( 1) SS BOND : angle 0.77875 ( 2) hydrogen bonds : bond 0.05568 ( 733) hydrogen bonds : angle 4.72786 ( 1999) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 355 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 877 MET cc_start: 0.7516 (mmm) cc_final: 0.7293 (mmt) REVERT: B 134 LYS cc_start: 0.8374 (tptp) cc_final: 0.8131 (tttp) REVERT: B 310 GLU cc_start: 0.7933 (mp0) cc_final: 0.7552 (mp0) REVERT: B 462 MET cc_start: 0.8463 (mmm) cc_final: 0.8220 (mmm) REVERT: C 86 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6572 (mm) outliers start: 77 outliers final: 47 residues processed: 403 average time/residue: 0.6057 time to fit residues: 267.6348 Evaluate side-chains 386 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 338 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 910 MET Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1222 GLN Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 430 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 179 optimal weight: 5.9990 chunk 44 optimal weight: 0.0670 chunk 150 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 59 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 468 ASN A 564 GLN A 736 ASN A 843 GLN A1157 ASN A1175 GLN B 195 ASN B 261 GLN B 404 ASN C 339 ASN C 400 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.124987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.116656 restraints weight = 26251.061| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.40 r_work: 0.3593 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15752 Z= 0.131 Angle : 0.590 9.671 21549 Z= 0.309 Chirality : 0.041 0.162 2322 Planarity : 0.005 0.046 2602 Dihedral : 14.317 81.840 2460 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 4.65 % Allowed : 19.25 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.20), residues: 1758 helix: 1.65 (0.19), residues: 743 sheet: 1.28 (0.30), residues: 243 loop : -0.31 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 628 TYR 0.019 0.001 TYR A1166 PHE 0.020 0.001 PHE A 197 TRP 0.019 0.001 TRP A 175 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00289 (15751) covalent geometry : angle 0.59008 (21547) SS BOND : bond 0.00327 ( 1) SS BOND : angle 0.43330 ( 2) hydrogen bonds : bond 0.04481 ( 733) hydrogen bonds : angle 4.50577 ( 1999) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 362 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 309 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7446 (mpp80) REVERT: A 877 MET cc_start: 0.7491 (mmm) cc_final: 0.7272 (mmt) REVERT: A 896 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7964 (mt) REVERT: B 134 LYS cc_start: 0.8356 (tptp) cc_final: 0.8105 (tttp) REVERT: B 158 GLN cc_start: -0.3023 (OUTLIER) cc_final: -0.3593 (mt0) REVERT: C 86 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6594 (mm) outliers start: 72 outliers final: 43 residues processed: 407 average time/residue: 0.6136 time to fit residues: 273.3596 Evaluate side-chains 385 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 338 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 453 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 160 optimal weight: 0.0070 chunk 130 optimal weight: 0.1980 chunk 75 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 171 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 468 ASN A 564 GLN A 736 ASN A 843 GLN A1175 GLN B 195 ASN B 261 GLN B 400 GLN B 404 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.126947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.118567 restraints weight = 26400.228| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.41 r_work: 0.3623 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15752 Z= 0.114 Angle : 0.566 9.945 21549 Z= 0.295 Chirality : 0.040 0.162 2322 Planarity : 0.004 0.046 2602 Dihedral : 14.229 75.206 2460 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 3.94 % Allowed : 20.61 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1758 helix: 1.78 (0.19), residues: 752 sheet: 1.44 (0.30), residues: 250 loop : -0.23 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 628 TYR 0.015 0.001 TYR A1166 PHE 0.018 0.001 PHE A 197 TRP 0.023 0.001 TRP A 175 HIS 0.003 0.001 HIS A 659 Details of bonding type rmsd covalent geometry : bond 0.00245 (15751) covalent geometry : angle 0.56620 (21547) SS BOND : bond 0.00270 ( 1) SS BOND : angle 0.39217 ( 2) hydrogen bonds : bond 0.03852 ( 733) hydrogen bonds : angle 4.32283 ( 1999) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 363 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7182 (mm-30) REVERT: A 539 PHE cc_start: 0.8165 (t80) cc_final: 0.7906 (t80) REVERT: A 877 MET cc_start: 0.7470 (mmm) cc_final: 0.7259 (mmt) REVERT: B 134 LYS cc_start: 0.8339 (tptp) cc_final: 0.8083 (tttp) REVERT: B 158 GLN cc_start: -0.3016 (OUTLIER) cc_final: -0.3611 (mt0) REVERT: B 185 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7875 (mm) REVERT: C 86 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6556 (mm) outliers start: 61 outliers final: 31 residues processed: 406 average time/residue: 0.5907 time to fit residues: 263.3690 Evaluate side-chains 380 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 345 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 426 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 71 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 153 optimal weight: 0.0020 chunk 42 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 270 ASN A 277 HIS A 468 ASN A 564 GLN A 736 ASN A 843 GLN A1157 ASN A1175 GLN B 195 ASN B 261 GLN B 404 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.122937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114632 restraints weight = 25946.805| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.40 r_work: 0.3562 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15752 Z= 0.200 Angle : 0.675 10.503 21549 Z= 0.354 Chirality : 0.045 0.184 2322 Planarity : 0.005 0.045 2602 Dihedral : 14.353 82.177 2460 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.04 % Favored : 95.90 % Rotamer: Outliers : 4.78 % Allowed : 20.48 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.20), residues: 1758 helix: 1.40 (0.19), residues: 755 sheet: 1.14 (0.31), residues: 241 loop : -0.33 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 361 TYR 0.024 0.002 TYR A1166 PHE 0.021 0.002 PHE A 197 TRP 0.022 0.002 TRP A 175 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00455 (15751) covalent geometry : angle 0.67546 (21547) SS BOND : bond 0.00597 ( 1) SS BOND : angle 0.82055 ( 2) hydrogen bonds : bond 0.05460 ( 733) hydrogen bonds : angle 4.65115 ( 1999) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 345 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7213 (mm-30) REVERT: A 877 MET cc_start: 0.7525 (mmm) cc_final: 0.7306 (mmt) REVERT: B 134 LYS cc_start: 0.8369 (tptp) cc_final: 0.8130 (tttm) REVERT: B 158 GLN cc_start: -0.2950 (OUTLIER) cc_final: -0.3543 (mt0) REVERT: B 310 GLU cc_start: 0.8019 (mp0) cc_final: 0.7583 (mp0) REVERT: C 86 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6563 (mm) outliers start: 74 outliers final: 47 residues processed: 397 average time/residue: 0.5941 time to fit residues: 259.2418 Evaluate side-chains 389 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 339 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 434 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 137 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 87 optimal weight: 0.0870 chunk 165 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 162 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1175 GLN B 195 ASN B 261 GLN B 339 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.124857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.116543 restraints weight = 26266.509| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.40 r_work: 0.3590 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15752 Z= 0.140 Angle : 0.619 9.699 21549 Z= 0.322 Chirality : 0.042 0.186 2322 Planarity : 0.005 0.044 2602 Dihedral : 14.283 78.156 2460 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 4.33 % Allowed : 20.74 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.20), residues: 1758 helix: 1.53 (0.19), residues: 755 sheet: 1.31 (0.30), residues: 243 loop : -0.32 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 203 TYR 0.024 0.002 TYR A1166 PHE 0.018 0.001 PHE A 197 TRP 0.027 0.001 TRP A 175 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00313 (15751) covalent geometry : angle 0.61935 (21547) SS BOND : bond 0.00376 ( 1) SS BOND : angle 0.48974 ( 2) hydrogen bonds : bond 0.04526 ( 733) hydrogen bonds : angle 4.50677 ( 1999) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 341 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7184 (mm-30) REVERT: A 877 MET cc_start: 0.7498 (mmm) cc_final: 0.7277 (mmt) REVERT: B 134 LYS cc_start: 0.8357 (tptp) cc_final: 0.8111 (tttp) REVERT: B 158 GLN cc_start: -0.2811 (OUTLIER) cc_final: -0.3410 (mt0) REVERT: B 310 GLU cc_start: 0.8021 (mp0) cc_final: 0.7548 (mp0) REVERT: C 86 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6575 (mm) outliers start: 67 outliers final: 47 residues processed: 388 average time/residue: 0.5981 time to fit residues: 255.0589 Evaluate side-chains 388 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 338 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 434 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 41 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1157 ASN A1175 GLN B 195 ASN B 261 GLN B 355 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.123198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.114897 restraints weight = 26028.834| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.41 r_work: 0.3566 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15752 Z= 0.189 Angle : 0.679 9.785 21549 Z= 0.353 Chirality : 0.044 0.167 2322 Planarity : 0.005 0.044 2602 Dihedral : 14.351 80.976 2460 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.68 % Rotamer: Outliers : 4.39 % Allowed : 20.74 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.20), residues: 1758 helix: 1.38 (0.19), residues: 756 sheet: 1.18 (0.31), residues: 235 loop : -0.41 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 203 TYR 0.023 0.002 TYR A1166 PHE 0.020 0.002 PHE A 197 TRP 0.033 0.002 TRP A 175 HIS 0.004 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00431 (15751) covalent geometry : angle 0.67868 (21547) SS BOND : bond 0.00527 ( 1) SS BOND : angle 0.79077 ( 2) hydrogen bonds : bond 0.05251 ( 733) hydrogen bonds : angle 4.64279 ( 1999) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 342 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7306 (mm-30) REVERT: A 877 MET cc_start: 0.7549 (mmm) cc_final: 0.7323 (mmt) REVERT: B 134 LYS cc_start: 0.8378 (tptp) cc_final: 0.8123 (tttm) REVERT: B 158 GLN cc_start: -0.2983 (OUTLIER) cc_final: -0.3558 (mt0) REVERT: B 310 GLU cc_start: 0.8029 (mp0) cc_final: 0.7568 (mp0) REVERT: C 86 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6563 (mm) outliers start: 68 outliers final: 50 residues processed: 388 average time/residue: 0.5922 time to fit residues: 252.9609 Evaluate side-chains 388 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 434 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 8 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 95 optimal weight: 0.3980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1157 ASN A1175 GLN B 195 ASN B 261 GLN B 355 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.124311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.116009 restraints weight = 26187.414| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.40 r_work: 0.3583 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15752 Z= 0.157 Angle : 0.656 10.847 21549 Z= 0.340 Chirality : 0.043 0.173 2322 Planarity : 0.005 0.046 2602 Dihedral : 14.324 79.348 2460 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.75 % Favored : 96.19 % Rotamer: Outliers : 4.01 % Allowed : 21.25 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.20), residues: 1758 helix: 1.45 (0.19), residues: 755 sheet: 1.28 (0.31), residues: 234 loop : -0.35 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 203 TYR 0.023 0.002 TYR A1166 PHE 0.020 0.002 PHE A1092 TRP 0.040 0.001 TRP A 175 HIS 0.006 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00354 (15751) covalent geometry : angle 0.65647 (21547) SS BOND : bond 0.00408 ( 1) SS BOND : angle 0.54196 ( 2) hydrogen bonds : bond 0.04789 ( 733) hydrogen bonds : angle 4.57459 ( 1999) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 343 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7306 (mm-30) REVERT: A 877 MET cc_start: 0.7516 (mmm) cc_final: 0.7294 (mmt) REVERT: B 134 LYS cc_start: 0.8374 (tptp) cc_final: 0.8136 (tttm) REVERT: B 158 GLN cc_start: -0.3112 (OUTLIER) cc_final: -0.3455 (tt0) REVERT: B 310 GLU cc_start: 0.8010 (mp0) cc_final: 0.7519 (mp0) REVERT: C 86 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6555 (mm) outliers start: 62 outliers final: 51 residues processed: 385 average time/residue: 0.5950 time to fit residues: 251.6478 Evaluate side-chains 393 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 339 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1171 ASN Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 434 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 5 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 95 optimal weight: 0.0870 chunk 73 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 overall best weight: 2.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 GLN A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1157 ASN A1175 GLN B 195 ASN B 261 GLN B 355 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.123070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.114778 restraints weight = 26007.134| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.40 r_work: 0.3565 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15752 Z= 0.189 Angle : 0.691 13.287 21549 Z= 0.360 Chirality : 0.044 0.167 2322 Planarity : 0.005 0.046 2602 Dihedral : 14.398 82.069 2460 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.44 % Favored : 95.51 % Rotamer: Outliers : 4.39 % Allowed : 20.87 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1758 helix: 1.32 (0.19), residues: 755 sheet: 1.13 (0.31), residues: 235 loop : -0.41 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 203 TYR 0.022 0.002 TYR A1166 PHE 0.021 0.002 PHE A1092 TRP 0.042 0.002 TRP A 175 HIS 0.005 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00432 (15751) covalent geometry : angle 0.69089 (21547) SS BOND : bond 0.00541 ( 1) SS BOND : angle 0.71927 ( 2) hydrogen bonds : bond 0.05313 ( 733) hydrogen bonds : angle 4.67705 ( 1999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6708.66 seconds wall clock time: 114 minutes 26.59 seconds (6866.59 seconds total)