Starting phenix.real_space_refine on Fri Jun 13 19:51:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d33_27154/06_2025/8d33_27154.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d33_27154/06_2025/8d33_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_27154/06_2025/8d33_27154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d33_27154/06_2025/8d33_27154.map" model { file = "/net/cci-nas-00/data/ceres_data/8d33_27154/06_2025/8d33_27154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d33_27154/06_2025/8d33_27154.cif" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.325 sd= 0.631 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 49 5.49 5 S 82 5.16 5 C 9585 2.51 5 N 2683 2.21 5 O 2872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15272 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7778 Classifications: {'peptide': 974} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 65, 'TRANS': 908} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3307 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 392} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3213 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "T" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 494 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' CA': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.86, per 1000 atoms: 0.65 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: 6.16 Conformation dependent library (CDL) restraints added in 1.9 seconds 3516 Ramachandran restraints generated. 1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3322 Finding SS restraints... 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: 6.40 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: 7.33 Time building geometry restraints manager: 6.08 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: 128.540 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: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 44.960 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 188.620 ------------------------------------------------------------------------------- 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 : 4.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 0.39 % Allowed : 4.39 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.21), residues: 1758 helix: 1.34 (0.20), residues: 739 sheet: 0.94 (0.31), residues: 242 loop : -0.16 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 220 HIS 0.002 0.001 HIS C 187 PHE 0.014 0.001 PHE A 197 TYR 0.009 0.001 TYR A1108 ARG 0.003 0.000 ARG A 574 Details of bonding type rmsd hydrogen bonds : bond 0.15236 ( 733) hydrogen bonds : angle 6.12378 ( 1999) SS BOND : bond 0.00604 ( 1) SS BOND : angle 0.99494 ( 2) covalent geometry : bond 0.00330 (15751) covalent geometry : angle 0.54555 (21547) *********************** 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 : 1.711 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: 1.4015 time to fit residues: 754.3803 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 : 1.923 ------------------------------------------------------------------------------- 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 152 optimal weight: 7.9990 chunk 137 optimal weight: 0.1980 chunk 76 optimal weight: 0.6980 chunk 46 optimal weight: 0.0870 chunk 92 optimal weight: 0.0570 chunk 73 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN A 264 GLN A 398 GLN A 564 GLN A 736 ASN A 843 GLN A1098 ASN A1157 ASN A1175 GLN B 195 ASN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.128930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.120451 restraints weight = 26043.988| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.40 r_work: 0.3651 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15752 Z= 0.122 Angle : 0.565 8.741 21549 Z= 0.296 Chirality : 0.041 0.160 2322 Planarity : 0.004 0.038 2602 Dihedral : 13.735 73.903 2460 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.50 % Favored : 97.44 % Rotamer: Outliers : 2.33 % Allowed : 15.57 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.20), residues: 1758 helix: 1.92 (0.19), residues: 745 sheet: 1.27 (0.31), residues: 244 loop : 0.01 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 175 HIS 0.003 0.001 HIS A 71 PHE 0.021 0.001 PHE A 197 TYR 0.017 0.001 TYR C 206 ARG 0.008 0.001 ARG A 657 Details of bonding type rmsd hydrogen bonds : bond 0.04484 ( 733) hydrogen bonds : angle 4.48480 ( 1999) SS BOND : bond 0.00206 ( 1) SS BOND : angle 0.31346 ( 2) covalent geometry : bond 0.00252 (15751) covalent geometry : angle 0.56476 (21547) *********************** 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 436 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 400 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 543 VAL cc_start: 0.8599 (p) cc_final: 0.8385 (t) REVERT: A 608 ASP cc_start: 0.7340 (t0) cc_final: 0.7135 (t0) REVERT: A 775 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7659 (mm-30) REVERT: A 877 MET cc_start: 0.7502 (mmm) cc_final: 0.7301 (mmt) REVERT: B 134 LYS cc_start: 0.8388 (tptp) cc_final: 0.8134 (tttp) REVERT: B 310 GLU cc_start: 0.7900 (mp0) cc_final: 0.7515 (mp0) REVERT: B 462 MET cc_start: 0.8481 (mmm) cc_final: 0.8251 (mmm) REVERT: B 473 ASP cc_start: 0.7759 (m-30) cc_final: 0.7526 (m-30) REVERT: C 129 ASP cc_start: 0.7033 (t70) cc_final: 0.6752 (t0) outliers start: 36 outliers final: 9 residues processed: 414 average time/residue: 1.3792 time to fit residues: 630.9930 Evaluate side-chains 368 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 359 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 799 SER Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 463 LYS Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 258 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 178 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 564 GLN A 736 ASN A 843 GLN A1157 ASN A1175 GLN B 195 ASN B 261 GLN B 323 HIS C 339 ASN C 400 GLN C 409 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.122270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.113941 restraints weight = 25992.215| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.39 r_work: 0.3552 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 15752 Z= 0.254 Angle : 0.722 9.520 21549 Z= 0.382 Chirality : 0.048 0.171 2322 Planarity : 0.007 0.078 2602 Dihedral : 14.321 82.055 2460 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 4.39 % Allowed : 17.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1758 helix: 1.37 (0.19), residues: 743 sheet: 1.04 (0.31), residues: 233 loop : -0.39 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 175 HIS 0.006 0.002 HIS B 96 PHE 0.029 0.003 PHE A 197 TYR 0.020 0.003 TYR A 649 ARG 0.009 0.001 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.06426 ( 733) hydrogen bonds : angle 4.86818 ( 1999) SS BOND : bond 0.00817 ( 1) SS BOND : angle 0.99776 ( 2) covalent geometry : bond 0.00581 (15751) covalent geometry : angle 0.72220 (21547) *********************** 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 423 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 355 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: A 383 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.6722 (mmmt) REVERT: A 543 VAL cc_start: 0.8704 (p) cc_final: 0.8401 (t) REVERT: A 608 ASP cc_start: 0.7519 (t0) cc_final: 0.7279 (t0) REVERT: A 877 MET cc_start: 0.7584 (mmm) cc_final: 0.7366 (mmt) REVERT: B 134 LYS cc_start: 0.8394 (tptp) cc_final: 0.8152 (tttp) REVERT: B 389 ARG cc_start: 0.5712 (OUTLIER) cc_final: 0.5438 (pmt170) REVERT: C 86 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6592 (mm) outliers start: 68 outliers final: 38 residues processed: 391 average time/residue: 1.3192 time to fit residues: 565.8662 Evaluate side-chains 381 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 340 time to evaluate : 1.780 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 548 CYS 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 844 VAL Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 921 LEU 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 1083 LEU Chi-restraints excluded: chain A residue 1121 GLU Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 236 GLU 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 C residue 71 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 164 LYS 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 394 GLU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 92 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 173 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 25 optimal weight: 6.9990 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 270 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 C 422 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.123198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.114875 restraints weight = 25920.866| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.40 r_work: 0.3567 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15752 Z= 0.187 Angle : 0.648 9.907 21549 Z= 0.342 Chirality : 0.044 0.166 2322 Planarity : 0.005 0.048 2602 Dihedral : 14.338 83.635 2460 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 4.72 % Allowed : 17.70 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.20), residues: 1758 helix: 1.41 (0.19), residues: 745 sheet: 1.06 (0.31), residues: 232 loop : -0.39 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 175 HIS 0.003 0.001 HIS A 805 PHE 0.025 0.002 PHE A 197 TYR 0.017 0.002 TYR A 150 ARG 0.005 0.001 ARG A 628 Details of bonding type rmsd hydrogen bonds : bond 0.05501 ( 733) hydrogen bonds : angle 4.71445 ( 1999) SS BOND : bond 0.00576 ( 1) SS BOND : angle 0.71579 ( 2) covalent geometry : bond 0.00421 (15751) covalent geometry : angle 0.64849 (21547) *********************** 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 428 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 355 time to evaluate : 1.607 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7236 (mm-30) REVERT: A 608 ASP cc_start: 0.7489 (t0) cc_final: 0.7251 (t0) REVERT: A 775 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7761 (mm-30) REVERT: A 877 MET cc_start: 0.7551 (mmm) cc_final: 0.7330 (mmt) REVERT: B 134 LYS cc_start: 0.8365 (tptp) cc_final: 0.8128 (tttp) REVERT: B 389 ARG cc_start: 0.5762 (OUTLIER) cc_final: 0.5527 (pmt170) REVERT: C 86 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6638 (mm) outliers start: 73 outliers final: 40 residues processed: 396 average time/residue: 1.3323 time to fit residues: 579.5957 Evaluate side-chains 386 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 343 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 534 SER Chi-restraints excluded: chain A residue 553 LYS 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 826 ILE 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 1083 LEU 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 B residue 86 LEU 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 236 GLU 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 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 31 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 468 ASN A 564 GLN A 736 ASN A 843 GLN A1175 GLN B 195 ASN B 261 GLN C 339 ASN C 400 GLN C 409 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.123924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.115517 restraints weight = 26321.196| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.42 r_work: 0.3578 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15752 Z= 0.157 Angle : 0.619 9.669 21549 Z= 0.325 Chirality : 0.043 0.167 2322 Planarity : 0.005 0.042 2602 Dihedral : 14.318 83.158 2460 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Rotamer: Outliers : 4.52 % Allowed : 18.80 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1758 helix: 1.48 (0.19), residues: 750 sheet: 1.09 (0.30), residues: 250 loop : -0.34 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 175 HIS 0.003 0.001 HIS A 71 PHE 0.022 0.002 PHE A 197 TYR 0.016 0.002 TYR A 150 ARG 0.006 0.000 ARG A 628 Details of bonding type rmsd hydrogen bonds : bond 0.04970 ( 733) hydrogen bonds : angle 4.59875 ( 1999) SS BOND : bond 0.00471 ( 1) SS BOND : angle 0.64606 ( 2) covalent geometry : bond 0.00350 (15751) covalent geometry : angle 0.61923 (21547) *********************** 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 419 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 349 time to evaluate : 1.616 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7242 (mm-30) REVERT: A 309 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7437 (mpp80) REVERT: A 608 ASP cc_start: 0.7473 (t0) cc_final: 0.7218 (t0) REVERT: A 877 MET cc_start: 0.7535 (mmm) cc_final: 0.7318 (mmt) REVERT: B 134 LYS cc_start: 0.8359 (tptp) cc_final: 0.8120 (tttp) REVERT: B 310 GLU cc_start: 0.8037 (mp0) cc_final: 0.7639 (mp0) REVERT: C 86 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6623 (mm) outliers start: 70 outliers final: 44 residues processed: 391 average time/residue: 1.5091 time to fit residues: 648.4665 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 : 1.601 ------------------------------------------------------------------------------- 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 309 ARG 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 534 SER Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 553 LYS 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 921 LEU 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 1083 LEU 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 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 236 GLU 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 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 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 159 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 277 HIS A 468 ASN A 564 GLN A 736 ASN A 843 GLN A1175 GLN B 195 ASN B 261 GLN B 339 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 = 0.3745 r_free = 0.3745 target = 0.120923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.112709 restraints weight = 26201.126| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.40 r_work: 0.3534 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 15752 Z= 0.268 Angle : 0.752 10.521 21549 Z= 0.396 Chirality : 0.049 0.163 2322 Planarity : 0.007 0.058 2602 Dihedral : 14.575 86.832 2460 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.38 % Favored : 95.56 % Rotamer: Outliers : 5.81 % Allowed : 18.15 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1758 helix: 1.02 (0.19), residues: 751 sheet: 0.96 (0.31), residues: 232 loop : -0.58 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 175 HIS 0.006 0.002 HIS B 96 PHE 0.023 0.003 PHE A 197 TYR 0.021 0.003 TYR A1166 ARG 0.006 0.001 ARG A 628 Details of bonding type rmsd hydrogen bonds : bond 0.06539 ( 733) hydrogen bonds : angle 4.93743 ( 1999) SS BOND : bond 0.00807 ( 1) SS BOND : angle 0.93414 ( 2) covalent geometry : bond 0.00613 (15751) covalent geometry : angle 0.75245 (21547) *********************** 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 433 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 343 time to evaluate : 1.583 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: A 608 ASP cc_start: 0.7604 (t0) cc_final: 0.7354 (t0) REVERT: A 877 MET cc_start: 0.7598 (mmm) cc_final: 0.7376 (mmt) REVERT: A 1145 ASP cc_start: 0.7700 (m-30) cc_final: 0.7491 (m-30) REVERT: B 134 LYS cc_start: 0.8373 (tptp) cc_final: 0.8123 (tttm) REVERT: B 158 GLN cc_start: -0.3015 (OUTLIER) cc_final: -0.3572 (mt0) REVERT: C 134 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7729 (ptpt) outliers start: 90 outliers final: 59 residues processed: 402 average time/residue: 1.2894 time to fit residues: 569.3183 Evaluate side-chains 393 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 331 time to evaluate : 1.703 ------------------------------------------------------------------------------- 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 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 474 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 553 LYS 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 826 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1050 LYS 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 1083 LEU 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 86 LEU 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 213 VAL 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 253 ASP 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 134 LYS 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 243 THR 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 387 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 430 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 164 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 564 GLN A 736 ASN A 843 GLN A1175 GLN B 195 ASN B 261 GLN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.122245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.114001 restraints weight = 26327.275| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.40 r_work: 0.3556 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15752 Z= 0.199 Angle : 0.686 9.690 21549 Z= 0.359 Chirality : 0.045 0.164 2322 Planarity : 0.006 0.048 2602 Dihedral : 14.532 86.666 2460 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.75 % Favored : 96.19 % Rotamer: Outliers : 5.10 % Allowed : 19.77 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.20), residues: 1758 helix: 1.15 (0.19), residues: 750 sheet: 0.90 (0.31), residues: 235 loop : -0.55 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 175 HIS 0.004 0.001 HIS B 96 PHE 0.021 0.002 PHE A 197 TYR 0.019 0.002 TYR A1166 ARG 0.007 0.001 ARG A 628 Details of bonding type rmsd hydrogen bonds : bond 0.05623 ( 733) hydrogen bonds : angle 4.79480 ( 1999) SS BOND : bond 0.00595 ( 1) SS BOND : angle 0.80266 ( 2) covalent geometry : bond 0.00450 (15751) covalent geometry : angle 0.68594 (21547) *********************** 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 416 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 337 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7373 (mm-30) REVERT: A 608 ASP cc_start: 0.7554 (t0) cc_final: 0.7297 (t0) REVERT: A 877 MET cc_start: 0.7567 (mmm) cc_final: 0.7321 (mmt) REVERT: A 1145 ASP cc_start: 0.7662 (m-30) cc_final: 0.7457 (m-30) REVERT: B 134 LYS cc_start: 0.8356 (tptp) cc_final: 0.8122 (tttp) REVERT: B 158 GLN cc_start: -0.2996 (OUTLIER) cc_final: -0.3539 (mt0) REVERT: B 310 GLU cc_start: 0.8017 (mp0) cc_final: 0.7585 (mp0) REVERT: C 107 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7901 (ttm-80) outliers start: 79 outliers final: 54 residues processed: 386 average time/residue: 1.2845 time to fit residues: 545.7126 Evaluate side-chains 387 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 330 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 475 SER Chi-restraints excluded: chain A residue 533 CYS Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 992 LEU 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 1083 LEU 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 1164 PHE Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1222 GLN Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 86 LEU 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 236 GLU Chi-restraints excluded: chain B residue 253 ASP 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 107 ARG 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 156 ILE 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 387 VAL Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 430 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 141 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 47 optimal weight: 0.0980 chunk 174 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 339 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 = 0.3790 r_free = 0.3790 target = 0.124069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.115789 restraints weight = 26071.005| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.40 r_work: 0.3584 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15752 Z= 0.144 Angle : 0.630 10.115 21549 Z= 0.329 Chirality : 0.042 0.162 2322 Planarity : 0.005 0.045 2602 Dihedral : 14.419 82.006 2460 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.36 % Rotamer: Outliers : 4.52 % Allowed : 20.74 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.20), residues: 1758 helix: 1.44 (0.19), residues: 750 sheet: 1.11 (0.31), residues: 239 loop : -0.42 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 175 HIS 0.003 0.001 HIS A 71 PHE 0.023 0.002 PHE C 254 TYR 0.016 0.002 TYR A1166 ARG 0.005 0.000 ARG A 628 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 733) hydrogen bonds : angle 4.59866 ( 1999) SS BOND : bond 0.00385 ( 1) SS BOND : angle 0.58805 ( 2) covalent geometry : bond 0.00322 (15751) covalent geometry : angle 0.63029 (21547) *********************** 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 417 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 347 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7375 (mm-30) REVERT: A 309 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7445 (mpp80) REVERT: A 608 ASP cc_start: 0.7475 (t0) cc_final: 0.7211 (t0) REVERT: A 877 MET cc_start: 0.7562 (mmm) cc_final: 0.7320 (mmt) REVERT: B 134 LYS cc_start: 0.8352 (tptp) cc_final: 0.8102 (tttp) REVERT: B 158 GLN cc_start: -0.3185 (OUTLIER) cc_final: -0.3608 (tt0) REVERT: B 310 GLU cc_start: 0.7999 (mp0) cc_final: 0.7525 (mp0) REVERT: C 86 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6598 (mm) REVERT: C 107 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7847 (ttm-80) outliers start: 70 outliers final: 45 residues processed: 393 average time/residue: 1.4161 time to fit residues: 608.9353 Evaluate side-chains 385 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 335 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 240 SER Chi-restraints excluded: chain A residue 309 ARG 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 534 SER Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 553 LYS 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 902 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 931 LEU 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 1164 PHE 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 253 ASP 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 107 ARG 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 270 ASN A 564 GLN A 736 ASN A 843 GLN A 906 HIS A1157 ASN A1175 GLN B 195 ASN B 261 GLN B 305 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN C 400 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.122858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.114594 restraints weight = 26096.434| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.40 r_work: 0.3563 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2664 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= 0.190 Angle : 0.681 14.162 21549 Z= 0.354 Chirality : 0.044 0.163 2322 Planarity : 0.006 0.046 2602 Dihedral : 14.477 83.447 2460 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.04 % Favored : 95.90 % Rotamer: Outliers : 5.10 % Allowed : 20.54 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1758 helix: 1.32 (0.19), residues: 751 sheet: 1.06 (0.31), residues: 233 loop : -0.50 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 175 HIS 0.004 0.001 HIS A 805 PHE 0.021 0.002 PHE A1092 TYR 0.016 0.002 TYR A1166 ARG 0.008 0.001 ARG A 628 Details of bonding type rmsd hydrogen bonds : bond 0.05396 ( 733) hydrogen bonds : angle 4.70227 ( 1999) SS BOND : bond 0.00566 ( 1) SS BOND : angle 0.77999 ( 2) covalent geometry : bond 0.00432 (15751) covalent geometry : angle 0.68080 (21547) *********************** 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 418 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 339 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: A 309 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7455 (mpp80) REVERT: A 608 ASP cc_start: 0.7501 (t0) cc_final: 0.7247 (t0) REVERT: A 877 MET cc_start: 0.7581 (mmm) cc_final: 0.7337 (mmt) REVERT: B 134 LYS cc_start: 0.8361 (tptp) cc_final: 0.8109 (tttm) REVERT: B 158 GLN cc_start: -0.3160 (OUTLIER) cc_final: -0.3689 (mt0) REVERT: B 310 GLU cc_start: 0.8034 (mp0) cc_final: 0.7644 (mp0) REVERT: C 86 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6563 (mm) REVERT: C 107 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7855 (ttm-80) outliers start: 79 outliers final: 55 residues processed: 388 average time/residue: 1.3906 time to fit residues: 595.4359 Evaluate side-chains 396 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 336 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 240 SER Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 309 ARG 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 534 SER Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 553 LYS 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 849 THR Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 931 LEU 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 1164 PHE 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 253 ASP 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 107 ARG 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 243 THR 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 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 41 optimal weight: 4.9990 chunk 130 optimal weight: 0.1980 chunk 42 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 151 optimal weight: 0.0670 chunk 134 optimal weight: 2.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 305 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.125831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.117546 restraints weight = 26524.677| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.41 r_work: 0.3609 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15752 Z= 0.125 Angle : 0.612 14.040 21549 Z= 0.315 Chirality : 0.041 0.168 2322 Planarity : 0.005 0.044 2602 Dihedral : 14.327 74.963 2460 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 3.42 % Allowed : 22.35 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.20), residues: 1758 helix: 1.56 (0.19), residues: 756 sheet: 1.38 (0.31), residues: 241 loop : -0.38 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 175 HIS 0.003 0.001 HIS A 659 PHE 0.019 0.001 PHE A1092 TYR 0.022 0.001 TYR A1166 ARG 0.008 0.000 ARG A 628 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 733) hydrogen bonds : angle 4.46472 ( 1999) SS BOND : bond 0.00276 ( 1) SS BOND : angle 0.42506 ( 2) covalent geometry : bond 0.00276 (15751) covalent geometry : angle 0.61178 (21547) ********************** 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 406 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 353 time to evaluate : 2.292 Fit side-chains revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7164 (mm-30) REVERT: A 608 ASP cc_start: 0.7388 (t0) cc_final: 0.7123 (t0) REVERT: A 877 MET cc_start: 0.7576 (mmm) cc_final: 0.7342 (mmt) REVERT: B 134 LYS cc_start: 0.8348 (tptp) cc_final: 0.8095 (tttp) REVERT: C 86 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6568 (mm) outliers start: 53 outliers final: 35 residues processed: 388 average time/residue: 1.3230 time to fit residues: 564.7426 Evaluate side-chains 379 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 342 time to evaluate : 1.680 ------------------------------------------------------------------------------- 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 240 SER 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 534 SER Chi-restraints excluded: chain A residue 541 GLN 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 902 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 931 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 1164 PHE Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 253 ASP 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 231 ILE Chi-restraints excluded: chain C residue 258 HIS Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 426 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 170 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 173 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 C 409 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.123182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.114898 restraints weight = 26071.748| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.41 r_work: 0.3567 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2703 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= 0.192 Angle : 0.683 14.534 21549 Z= 0.354 Chirality : 0.045 0.186 2322 Planarity : 0.006 0.048 2602 Dihedral : 14.416 79.099 2460 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 3.36 % Allowed : 22.55 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.20), residues: 1758 helix: 1.36 (0.19), residues: 754 sheet: 1.23 (0.31), residues: 233 loop : -0.42 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 175 HIS 0.004 0.001 HIS B 192 PHE 0.022 0.002 PHE A 407 TYR 0.024 0.002 TYR A1166 ARG 0.010 0.001 ARG A 657 Details of bonding type rmsd hydrogen bonds : bond 0.05286 ( 733) hydrogen bonds : angle 4.64781 ( 1999) SS BOND : bond 0.00608 ( 1) SS BOND : angle 0.81335 ( 2) covalent geometry : bond 0.00438 (15751) covalent geometry : angle 0.68307 (21547) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14554.00 seconds wall clock time: 252 minutes 42.75 seconds (15162.75 seconds total)