Starting phenix.real_space_refine on Fri Jul 3 12:31:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ic1_52824/07_2026/9ic1_52824.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ic1_52824/07_2026/9ic1_52824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ic1_52824/07_2026/9ic1_52824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ic1_52824/07_2026/9ic1_52824.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ic1_52824/07_2026/9ic1_52824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ic1_52824/07_2026/9ic1_52824.map" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.962 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 41 5.49 5 S 76 5.16 5 C 8904 2.51 5 N 2483 2.21 5 O 2677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14182 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 922, 7340 Classifications: {'peptide': 922} Link IDs: {'PTRANS': 62, 'TRANS': 859} Chain breaks: 6 Chain: "B" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2984 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 358} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3049 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 366} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 375 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "T" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 405 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'DCP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 2.89, per 1000 atoms: 0.20 Number of scatterers: 14182 At special positions: 0 Unit cell: (98.532, 99.36, 148.212, 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 76 16.00 P 41 15.00 O 2677 8.00 N 2483 7.00 C 8904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 487.0 milliseconds 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3134 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 13 sheets defined 48.8% alpha, 13.6% beta 17 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 80 through 88 removed outlier: 3.781A pdb=" N GLN A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix removed outlier: 3.729A pdb=" N LEU A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) 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 225 through 230 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.700A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.731A pdb=" N TYR A 282 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 283 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 316 removed outlier: 3.549A pdb=" N SER A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 351 removed outlier: 3.952A pdb=" N ASP A 349 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 351 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.502A pdb=" N LEU A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 removed outlier: 3.555A pdb=" N GLN A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.134A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 3.824A pdb=" N SER A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 475 removed outlier: 3.672A pdb=" N SER A 475 " --> pdb=" O GLN A 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 475' Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.681A pdb=" N LYS A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 554 removed outlier: 3.619A pdb=" N LEU A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 removed outlier: 3.839A pdb=" N LYS A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 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: 4.683A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 Processing helix chain 'A' and resid 858 through 862 Processing helix chain 'A' and resid 871 through 878 removed outlier: 4.328A pdb=" N LYS A 875 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 922 Processing helix chain 'A' and resid 930 through 940 removed outlier: 3.652A pdb=" N THR A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 955 Processing helix chain 'A' and resid 957 through 970 removed outlier: 3.735A pdb=" N PHE A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 962 " --> pdb=" O GLY A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 988 Processing helix chain 'A' and resid 1054 through 1066 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.610A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1168 removed outlier: 3.691A pdb=" N LEU A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1209 removed outlier: 4.015A pdb=" N ARG A1208 " --> pdb=" O THR A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1228 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.538A pdb=" N GLY B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 93 Processing helix chain 'B' and resid 123 through 128 removed outlier: 3.586A pdb=" N ILE B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 152 Processing helix chain 'B' and resid 159 through 166 Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 221 through 240 removed outlier: 3.981A pdb=" N PHE B 240 " --> pdb=" O TRP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 282 through 289 removed outlier: 4.274A pdb=" N THR B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.550A pdb=" N THR B 295 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.538A pdb=" N PHE B 328 " --> pdb=" O LEU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 383 removed outlier: 3.701A pdb=" N ASN B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 420 through 425 Processing helix chain 'B' and resid 444 through 458 removed outlier: 3.650A pdb=" N SER B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASN B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 57 through 60 Processing helix chain 'C' and resid 61 through 68 Processing helix chain 'C' and resid 74 through 94 Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 142 through 152 Processing helix chain 'C' and resid 159 through 166 Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 221 through 240 removed outlier: 4.092A pdb=" N PHE C 240 " --> pdb=" O TRP C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 316 through 327 Processing helix chain 'C' and resid 365 through 382 Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 418 through 425 removed outlier: 3.961A pdb=" N LEU C 422 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU C 423 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 459 removed outlier: 4.718A pdb=" N ASP C 447 " --> pdb=" O SER C 443 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.505A pdb=" N TRP A 175 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 438 removed outlier: 4.577A pdb=" N TYR A 837 " --> pdb=" O LEU A 816 " (cutoff:3.500A) 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 1131 removed outlier: 6.644A pdb=" N GLY A1127 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ARG A1142 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N PHE A1129 " --> pdb=" O LEU A1140 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU A1140 " --> pdb=" O PHE A1129 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 889 " --> pdb=" O VAL A1137 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP A1186 " --> pdb=" O LEU A 886 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A1216 " --> pdb=" O ILE A1185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 101 removed outlier: 6.031A pdb=" N PHE B 100 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE B 185 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE B 180 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE B 274 " --> pdb=" O ASP B 315 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LYS B 271 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE B 267 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TYR B 265 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU B 275 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 122 Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 300 removed outlier: 3.567A pdb=" N ASP B 300 " --> pdb=" O LYS B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 387 through 389 removed outlier: 6.653A pdb=" N VAL B 357 " --> pdb=" O TRP B 388 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA B 358 " --> pdb=" O VAL B 415 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 99 through 101 removed outlier: 6.178A pdb=" N PHE C 100 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ILE C 185 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL C 309 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE C 274 " --> pdb=" O ASP C 315 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR C 265 " --> pdb=" O PRO C 273 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS C 259 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER C 248 " --> pdb=" O TYR C 264 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 107 through 108 Processing sheet with id=AB3, first strand: chain 'C' and resid 298 through 300 Processing sheet with id=AB4, first strand: chain 'C' and resid 387 through 389 removed outlier: 7.115A pdb=" N VAL C 357 " --> pdb=" O TRP C 388 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ALA C 358 " --> pdb=" O VAL C 415 " (cutoff:3.500A) 638 hydrogen bonds defined for protein. 1794 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3894 1.33 - 1.45: 2709 1.45 - 1.57: 7812 1.57 - 1.69: 79 1.69 - 1.81: 118 Bond restraints: 14612 Sorted by residual: bond pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 1.746 1.606 0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" O3A DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 1.672 1.610 0.062 2.00e-02 2.50e+03 9.74e+00 bond pdb=" C3' DG T 17 " pdb=" C2' DG T 17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.77e+00 bond pdb=" C3' DG T 16 " pdb=" C2' DG T 16 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.46e+00 bond pdb=" C THR A 599 " pdb=" O THR A 599 " ideal model delta sigma weight residual 1.244 1.219 0.025 1.00e-02 1.00e+04 6.10e+00 ... (remaining 14607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 19761 2.23 - 4.47: 215 4.47 - 6.70: 7 6.70 - 8.94: 1 8.94 - 11.17: 1 Bond angle restraints: 19985 Sorted by residual: angle pdb=" N3 DT T 22 " pdb=" C4 DT T 22 " pdb=" O4 DT T 22 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT P 16 " pdb=" C4 DT P 16 " pdb=" O4 DT P 16 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT T 24 " pdb=" C4 DT T 24 " pdb=" O4 DT T 24 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" O4 DT T 22 " pdb=" C4 DT T 22 " pdb=" C5 DT T 22 " ideal model delta sigma weight residual 124.90 122.07 2.83 7.00e-01 2.04e+00 1.63e+01 angle pdb=" N3 DT P 25 " pdb=" C4 DT P 25 " pdb=" O4 DT P 25 " ideal model delta sigma weight residual 119.90 122.28 -2.38 6.00e-01 2.78e+00 1.57e+01 ... (remaining 19980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.56: 8347 28.56 - 57.12: 250 57.12 - 85.68: 15 85.68 - 114.24: 0 114.24 - 142.80: 2 Dihedral angle restraints: 8614 sinusoidal: 3766 harmonic: 4848 Sorted by residual: dihedral pdb=" CA ILE A1133 " pdb=" C ILE A1133 " pdb=" N HIS A1134 " pdb=" CA HIS A1134 " ideal model delta harmonic sigma weight residual -180.00 -159.89 -20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" C4' DG P 13 " pdb=" C3' DG P 13 " pdb=" O3' DG P 13 " pdb=" P DT P 14 " ideal model delta sinusoidal sigma weight residual 220.00 77.20 142.80 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" C4' DG P 8 " pdb=" C3' DG P 8 " pdb=" O3' DG P 8 " pdb=" P DT P 9 " ideal model delta sinusoidal sigma weight residual 220.00 77.37 142.63 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 8611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1685 0.043 - 0.086: 345 0.086 - 0.128: 138 0.128 - 0.171: 6 0.171 - 0.214: 2 Chirality restraints: 2176 Sorted by residual: chirality pdb=" C1' DCP A1302 " pdb=" C2' DCP A1302 " pdb=" N1 DCP A1302 " pdb=" O4' DCP A1302 " both_signs ideal model delta sigma weight residual False 2.25 2.46 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA VAL A 845 " pdb=" N VAL A 845 " pdb=" C VAL A 845 " pdb=" CB VAL A 845 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CA THR A 599 " pdb=" N THR A 599 " pdb=" C THR A 599 " pdb=" CB THR A 599 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 2173 not shown) Planarity restraints: 2427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 72 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO A 73 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 844 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C VAL A 844 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL A 844 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 845 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 349 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO B 350 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 350 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 350 " 0.020 5.00e-02 4.00e+02 ... (remaining 2424 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 392 2.71 - 3.26: 13644 3.26 - 3.80: 23197 3.80 - 4.35: 29947 4.35 - 4.90: 50144 Nonbonded interactions: 117324 Sorted by model distance: nonbonded pdb="CA CA A1301 " pdb=" O2G DCP A1302 " model vdw 2.160 3.250 nonbonded pdb=" OG SER C 431 " pdb=" OG1 THR C 434 " model vdw 2.217 3.040 nonbonded pdb=" OG SER A 272 " pdb=" O VAL A 844 " model vdw 2.218 3.040 nonbonded pdb="CA CA A1301 " pdb=" O1A DCP A1302 " model vdw 2.242 3.250 nonbonded pdb=" OD1 ASP A 904 " pdb=" OG1 THR A 914 " model vdw 2.267 3.040 ... (remaining 117319 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 42 through 458) selection = (chain 'C' and (resid 42 through 128 or resid 145 through 192 or resid 205 throu \ gh 458)) } 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: 3.240 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.200 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 0.140 14612 Z= 0.228 Angle : 0.548 11.174 19985 Z= 0.356 Chirality : 0.040 0.214 2176 Planarity : 0.004 0.046 2427 Dihedral : 12.802 142.799 5480 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.62 % Allowed : 2.89 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.21), residues: 1652 helix: 1.14 (0.20), residues: 714 sheet: 0.45 (0.35), residues: 240 loop : 0.47 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1190 TYR 0.008 0.001 TYR A 434 PHE 0.010 0.001 PHE A1180 TRP 0.008 0.001 TRP A1118 HIS 0.004 0.001 HIS C 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.23 (14612) covalent geometry : angle 0.54782 / 0.36 (19985) hydrogen bonds : bond 0.17060 / 10.94 ( 682) hydrogen bonds : angle 6.85903 / 4.76 ( 1878) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 272 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 950 ASN cc_start: 0.5642 (m-40) cc_final: 0.5169 (p0) REVERT: C 169 ASN cc_start: 0.6184 (m-40) cc_final: 0.5961 (p0) REVERT: C 366 THR cc_start: 0.7902 (m) cc_final: 0.7671 (p) REVERT: C 370 ARG cc_start: 0.7662 (ttm170) cc_final: 0.7425 (mmm-85) REVERT: C 428 GLN cc_start: 0.6913 (tt0) cc_final: 0.6551 (tm-30) outliers start: 9 outliers final: 5 residues processed: 279 average time/residue: 0.4500 time to fit residues: 139.2291 Evaluate side-chains 175 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 345 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN B 184 GLN B 190 HIS ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.171724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.132241 restraints weight = 19397.739| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 3.00 r_work: 0.3899 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14612 Z= 0.250 Angle : 0.656 12.312 19985 Z= 0.346 Chirality : 0.046 0.204 2176 Planarity : 0.006 0.052 2427 Dihedral : 14.476 145.774 2260 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.89 % Allowed : 10.33 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1652 helix: 0.88 (0.19), residues: 704 sheet: 0.31 (0.33), residues: 238 loop : 0.10 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 220 TYR 0.015 0.002 TYR A 150 PHE 0.015 0.002 PHE B 228 TRP 0.012 0.002 TRP A 220 HIS 0.010 0.002 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.25 (14612) covalent geometry : angle 0.65607 / 0.35 (19985) hydrogen bonds : bond 0.05214 / 3.44 ( 682) hydrogen bonds : angle 5.61931 / 3.96 ( 1878) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 137 GLN cc_start: 0.6319 (OUTLIER) cc_final: 0.5214 (mp10) REVERT: A 288 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6827 (mtm180) REVERT: A 354 ASN cc_start: 0.7832 (OUTLIER) cc_final: 0.7604 (m110) REVERT: A 469 ASP cc_start: 0.7544 (t0) cc_final: 0.7341 (t0) REVERT: A 832 ASP cc_start: 0.5895 (t0) cc_final: 0.5554 (t0) REVERT: A 950 ASN cc_start: 0.4850 (m-40) cc_final: 0.4349 (p0) REVERT: A 1208 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.6030 (mtm180) REVERT: B 215 TRP cc_start: 0.7784 (t-100) cc_final: 0.7013 (t-100) REVERT: B 379 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: B 401 GLN cc_start: 0.6917 (mt0) cc_final: 0.6687 (mt0) REVERT: C 107 GLN cc_start: 0.7131 (pt0) cc_final: 0.6640 (pm20) REVERT: C 119 PHE cc_start: 0.6873 (m-80) cc_final: 0.6575 (m-80) REVERT: C 169 ASN cc_start: 0.6218 (m-40) cc_final: 0.5773 (p0) REVERT: C 366 THR cc_start: 0.6912 (m) cc_final: 0.6688 (p) REVERT: C 370 ARG cc_start: 0.6984 (ttm170) cc_final: 0.6471 (mmm-85) REVERT: C 428 GLN cc_start: 0.5985 (tt0) cc_final: 0.5099 (tm-30) outliers start: 42 outliers final: 18 residues processed: 196 average time/residue: 0.4031 time to fit residues: 88.9627 Evaluate side-chains 178 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 108 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN B 297 GLN ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.174478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.135098 restraints weight = 19390.404| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 3.00 r_work: 0.3962 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14612 Z= 0.145 Angle : 0.549 8.035 19985 Z= 0.292 Chirality : 0.042 0.189 2176 Planarity : 0.005 0.049 2427 Dihedral : 14.253 145.791 2254 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.48 % Allowed : 11.98 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1652 helix: 0.97 (0.19), residues: 716 sheet: 0.27 (0.33), residues: 239 loop : 0.12 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 823 TYR 0.014 0.001 TYR A 150 PHE 0.015 0.001 PHE B 119 TRP 0.010 0.001 TRP A 220 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (14612) covalent geometry : angle 0.54921 / 0.29 (19985) hydrogen bonds : bond 0.04245 / 2.83 ( 682) hydrogen bonds : angle 5.24146 / 3.72 ( 1878) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 137 GLN cc_start: 0.6279 (OUTLIER) cc_final: 0.5221 (mp10) REVERT: A 288 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6761 (mtm180) REVERT: A 469 ASP cc_start: 0.7502 (t0) cc_final: 0.7292 (t0) REVERT: A 812 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7425 (ttt) REVERT: A 832 ASP cc_start: 0.5826 (t0) cc_final: 0.5520 (t0) REVERT: A 950 ASN cc_start: 0.4775 (m-40) cc_final: 0.4318 (p0) REVERT: B 97 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7523 (pp20) REVERT: B 214 VAL cc_start: 0.6888 (t) cc_final: 0.6639 (m) REVERT: B 215 TRP cc_start: 0.7683 (t-100) cc_final: 0.6923 (t-100) REVERT: B 297 GLN cc_start: 0.7823 (tt0) cc_final: 0.7605 (tt0) REVERT: B 379 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.6203 (mp0) REVERT: B 401 GLN cc_start: 0.6803 (mt0) cc_final: 0.6594 (mt0) REVERT: B 440 MET cc_start: 0.8191 (ttm) cc_final: 0.7871 (ttt) REVERT: B 442 ILE cc_start: 0.9031 (tt) cc_final: 0.8816 (tt) REVERT: C 47 CYS cc_start: 0.6101 (m) cc_final: 0.5735 (m) REVERT: C 107 GLN cc_start: 0.7074 (pt0) cc_final: 0.6619 (pm20) REVERT: C 119 PHE cc_start: 0.6847 (m-80) cc_final: 0.6546 (m-80) REVERT: C 169 ASN cc_start: 0.6243 (m-40) cc_final: 0.5877 (OUTLIER) REVERT: C 212 SER cc_start: 0.8214 (p) cc_final: 0.7961 (m) REVERT: C 366 THR cc_start: 0.6839 (m) cc_final: 0.6582 (p) REVERT: C 370 ARG cc_start: 0.7018 (ttm170) cc_final: 0.6524 (mmm-85) REVERT: C 428 GLN cc_start: 0.5919 (tt0) cc_final: 0.5058 (tm-30) outliers start: 36 outliers final: 18 residues processed: 193 average time/residue: 0.3945 time to fit residues: 85.5548 Evaluate side-chains 178 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 369 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 37 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN B 292 ASN C 190 HIS ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.163668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.124337 restraints weight = 19198.499| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.86 r_work: 0.3686 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14612 Z= 0.191 Angle : 0.577 8.020 19985 Z= 0.303 Chirality : 0.043 0.169 2176 Planarity : 0.005 0.049 2427 Dihedral : 14.260 146.045 2253 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.69 % Allowed : 13.02 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.20), residues: 1652 helix: 0.93 (0.19), residues: 710 sheet: 0.20 (0.34), residues: 231 loop : -0.05 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 546 TYR 0.017 0.002 TYR A1108 PHE 0.029 0.002 PHE A 766 TRP 0.012 0.001 TRP C 278 HIS 0.008 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (14612) covalent geometry : angle 0.57657 / 0.30 (19985) hydrogen bonds : bond 0.04243 / 2.81 ( 682) hydrogen bonds : angle 5.20228 / 3.69 ( 1878) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 137 GLN cc_start: 0.6670 (OUTLIER) cc_final: 0.5541 (mp10) REVERT: A 288 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6974 (mtm180) REVERT: A 354 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7562 (m110) REVERT: A 832 ASP cc_start: 0.6152 (t0) cc_final: 0.5819 (t0) REVERT: A 950 ASN cc_start: 0.5031 (m-40) cc_final: 0.4552 (p0) REVERT: A 1164 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6602 (m-80) REVERT: A 1223 ILE cc_start: 0.7079 (mt) cc_final: 0.6826 (mp) REVERT: B 92 MET cc_start: 0.7273 (tpt) cc_final: 0.7052 (mmt) REVERT: B 214 VAL cc_start: 0.7174 (t) cc_final: 0.6908 (m) REVERT: B 215 TRP cc_start: 0.7821 (t-100) cc_final: 0.7086 (t-100) REVERT: B 297 GLN cc_start: 0.7909 (tt0) cc_final: 0.7666 (tt0) REVERT: B 379 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6288 (mp0) REVERT: B 401 GLN cc_start: 0.6992 (mt0) cc_final: 0.6788 (mt0) REVERT: B 442 ILE cc_start: 0.9122 (tt) cc_final: 0.8920 (tt) REVERT: C 47 CYS cc_start: 0.6302 (m) cc_final: 0.5911 (m) REVERT: C 107 GLN cc_start: 0.7294 (pt0) cc_final: 0.6836 (pm20) REVERT: C 119 PHE cc_start: 0.6943 (m-80) cc_final: 0.6705 (m-80) REVERT: C 169 ASN cc_start: 0.6285 (m-40) cc_final: 0.5990 (OUTLIER) REVERT: C 355 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7850 (mp) REVERT: C 370 ARG cc_start: 0.7253 (ttm170) cc_final: 0.6792 (mmm-85) REVERT: C 428 GLN cc_start: 0.6162 (tt0) cc_final: 0.5328 (tm-30) outliers start: 39 outliers final: 20 residues processed: 180 average time/residue: 0.3684 time to fit residues: 75.2275 Evaluate side-chains 178 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 355 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 134 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.174479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.134233 restraints weight = 19347.520| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 3.08 r_work: 0.3937 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14612 Z= 0.167 Angle : 0.553 7.186 19985 Z= 0.291 Chirality : 0.042 0.171 2176 Planarity : 0.005 0.048 2427 Dihedral : 14.264 145.911 2253 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.55 % Allowed : 14.05 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.20), residues: 1652 helix: 0.92 (0.19), residues: 717 sheet: 0.16 (0.34), residues: 231 loop : -0.02 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 546 TYR 0.019 0.002 TYR A1108 PHE 0.020 0.002 PHE A 766 TRP 0.013 0.001 TRP C 278 HIS 0.007 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (14612) covalent geometry : angle 0.55294 / 0.29 (19985) hydrogen bonds : bond 0.04066 / 2.70 ( 682) hydrogen bonds : angle 5.12797 / 3.63 ( 1878) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 GLN cc_start: 0.6229 (OUTLIER) cc_final: 0.5220 (mp10) REVERT: A 288 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6945 (mtm180) REVERT: A 354 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7491 (m110) REVERT: A 832 ASP cc_start: 0.5757 (t0) cc_final: 0.5397 (t0) REVERT: A 950 ASN cc_start: 0.4759 (m-40) cc_final: 0.4309 (p0) REVERT: A 1164 PHE cc_start: 0.6638 (OUTLIER) cc_final: 0.6257 (m-80) REVERT: A 1208 ARG cc_start: 0.6481 (OUTLIER) cc_final: 0.5848 (mtm180) REVERT: B 214 VAL cc_start: 0.6925 (t) cc_final: 0.6662 (m) REVERT: B 215 TRP cc_start: 0.7625 (t-100) cc_final: 0.6834 (t-100) REVERT: B 292 ASN cc_start: 0.6865 (t0) cc_final: 0.6613 (t0) REVERT: B 297 GLN cc_start: 0.7958 (tt0) cc_final: 0.7751 (tt0) REVERT: B 379 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.6180 (mp0) REVERT: B 442 ILE cc_start: 0.9017 (tt) cc_final: 0.8816 (tt) REVERT: C 47 CYS cc_start: 0.5954 (m) cc_final: 0.5610 (m) REVERT: C 107 GLN cc_start: 0.7073 (pt0) cc_final: 0.6643 (pm20) REVERT: C 119 PHE cc_start: 0.6692 (m-80) cc_final: 0.6417 (m-80) REVERT: C 169 ASN cc_start: 0.6325 (m-40) cc_final: 0.5984 (p0) REVERT: C 210 GLU cc_start: 0.6779 (tt0) cc_final: 0.6022 (tm-30) REVERT: C 233 ARG cc_start: 0.6489 (mmt90) cc_final: 0.6280 (mpt90) REVERT: C 355 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7670 (mp) REVERT: C 370 ARG cc_start: 0.6928 (ttm170) cc_final: 0.6473 (mmm-85) REVERT: C 428 GLN cc_start: 0.5794 (tt0) cc_final: 0.4947 (tm-30) outliers start: 37 outliers final: 18 residues processed: 183 average time/residue: 0.3822 time to fit residues: 79.5373 Evaluate side-chains 181 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1164 PHE Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 162 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 152 optimal weight: 30.0000 chunk 153 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.162561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.124027 restraints weight = 19375.348| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.92 r_work: 0.3658 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14612 Z= 0.237 Angle : 0.609 7.630 19985 Z= 0.319 Chirality : 0.044 0.179 2176 Planarity : 0.005 0.049 2427 Dihedral : 14.336 145.754 2253 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.58 % Allowed : 13.57 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1652 helix: 0.78 (0.19), residues: 711 sheet: 0.05 (0.34), residues: 231 loop : -0.20 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 597 TYR 0.022 0.002 TYR A1108 PHE 0.024 0.002 PHE A 766 TRP 0.017 0.002 TRP C 278 HIS 0.009 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 (14612) covalent geometry : angle 0.60854 / 0.32 (19985) hydrogen bonds : bond 0.04445 / 2.94 ( 682) hydrogen bonds : angle 5.24195 / 3.71 ( 1878) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 159 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 137 GLN cc_start: 0.6779 (OUTLIER) cc_final: 0.5662 (mp10) REVERT: A 288 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.7075 (mtm180) REVERT: A 354 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7644 (m110) REVERT: A 413 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7409 (tt) REVERT: A 812 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7739 (ttt) REVERT: A 832 ASP cc_start: 0.6332 (t0) cc_final: 0.6008 (t0) REVERT: A 950 ASN cc_start: 0.5151 (m-40) cc_final: 0.4560 (p0) REVERT: A 1208 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6178 (mtm180) REVERT: B 214 VAL cc_start: 0.7299 (t) cc_final: 0.6988 (m) REVERT: B 215 TRP cc_start: 0.7817 (t-100) cc_final: 0.7053 (t-100) REVERT: B 292 ASN cc_start: 0.6927 (t0) cc_final: 0.6675 (t0) REVERT: B 297 GLN cc_start: 0.7952 (tt0) cc_final: 0.7708 (tt0) REVERT: B 379 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.6314 (mp0) REVERT: B 442 ILE cc_start: 0.9156 (tt) cc_final: 0.8948 (tt) REVERT: C 47 CYS cc_start: 0.6375 (m) cc_final: 0.6036 (m) REVERT: C 119 PHE cc_start: 0.7008 (m-80) cc_final: 0.6801 (m-80) REVERT: C 169 ASN cc_start: 0.6286 (m-40) cc_final: 0.6013 (p0) REVERT: C 210 GLU cc_start: 0.7458 (tt0) cc_final: 0.6664 (tm-30) REVERT: C 355 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7951 (mp) REVERT: C 370 ARG cc_start: 0.7280 (ttm170) cc_final: 0.6800 (mmm-85) outliers start: 52 outliers final: 21 residues processed: 191 average time/residue: 0.3767 time to fit residues: 81.8134 Evaluate side-chains 178 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 159 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.165116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.126027 restraints weight = 19016.437| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.85 r_work: 0.3708 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14612 Z= 0.137 Angle : 0.545 8.729 19985 Z= 0.286 Chirality : 0.041 0.195 2176 Planarity : 0.005 0.048 2427 Dihedral : 14.280 145.770 2253 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.55 % Allowed : 15.29 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.21), residues: 1652 helix: 0.95 (0.19), residues: 713 sheet: 0.13 (0.34), residues: 231 loop : -0.07 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 233 TYR 0.021 0.001 TYR A1108 PHE 0.016 0.001 PHE B 119 TRP 0.018 0.001 TRP C 278 HIS 0.007 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (14612) covalent geometry : angle 0.54519 / 0.29 (19985) hydrogen bonds : bond 0.03830 / 2.55 ( 682) hydrogen bonds : angle 5.06079 / 3.59 ( 1878) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 GLN cc_start: 0.6585 (OUTLIER) cc_final: 0.5404 (mp10) REVERT: A 288 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6986 (mtm180) REVERT: A 413 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7329 (tt) REVERT: A 812 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7552 (ttt) REVERT: A 832 ASP cc_start: 0.6199 (t0) cc_final: 0.5848 (t0) REVERT: A 950 ASN cc_start: 0.4979 (m-40) cc_final: 0.4407 (p0) REVERT: A 1191 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7442 (mmtt) REVERT: B 214 VAL cc_start: 0.7180 (t) cc_final: 0.6921 (m) REVERT: B 215 TRP cc_start: 0.7744 (t-100) cc_final: 0.6969 (t-100) REVERT: B 292 ASN cc_start: 0.6719 (t0) cc_final: 0.6482 (t0) REVERT: B 297 GLN cc_start: 0.7955 (tt0) cc_final: 0.7740 (tt0) REVERT: B 379 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6284 (mp0) REVERT: B 440 MET cc_start: 0.8398 (ttm) cc_final: 0.8138 (ttt) REVERT: C 47 CYS cc_start: 0.6256 (m) cc_final: 0.5922 (m) REVERT: C 48 ARG cc_start: 0.7812 (tpt90) cc_final: 0.7587 (tpt170) REVERT: C 107 GLN cc_start: 0.7387 (pt0) cc_final: 0.6974 (pm20) REVERT: C 119 PHE cc_start: 0.6945 (m-80) cc_final: 0.6649 (m-80) REVERT: C 169 ASN cc_start: 0.6323 (m-40) cc_final: 0.6120 (p0) REVERT: C 210 GLU cc_start: 0.7306 (tt0) cc_final: 0.6568 (tm-30) REVERT: C 215 TRP cc_start: 0.7425 (t-100) cc_final: 0.7066 (t-100) REVERT: C 242 MET cc_start: 0.4906 (ttp) cc_final: 0.4003 (mpm) REVERT: C 370 ARG cc_start: 0.7165 (ttm170) cc_final: 0.6698 (mmm-85) outliers start: 37 outliers final: 19 residues processed: 181 average time/residue: 0.3713 time to fit residues: 76.7437 Evaluate side-chains 174 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 34 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 137 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 0.0000 chunk 22 optimal weight: 4.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.163647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.124519 restraints weight = 19090.748| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.84 r_work: 0.3691 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14612 Z= 0.187 Angle : 0.579 9.138 19985 Z= 0.301 Chirality : 0.043 0.265 2176 Planarity : 0.005 0.048 2427 Dihedral : 14.304 145.844 2253 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.55 % Allowed : 15.50 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.20), residues: 1652 helix: 0.83 (0.19), residues: 713 sheet: 0.09 (0.35), residues: 231 loop : -0.15 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 597 TYR 0.030 0.002 TYR A 479 PHE 0.018 0.002 PHE A 766 TRP 0.024 0.001 TRP C 278 HIS 0.015 0.001 HIS C 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (14612) covalent geometry : angle 0.57861 / 0.30 (19985) hydrogen bonds : bond 0.04086 / 2.71 ( 682) hydrogen bonds : angle 5.11662 / 3.63 ( 1878) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 137 GLN cc_start: 0.6630 (OUTLIER) cc_final: 0.5459 (mp10) REVERT: A 229 VAL cc_start: 0.8063 (t) cc_final: 0.7814 (m) REVERT: A 288 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.7003 (mtm180) REVERT: A 413 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7299 (tt) REVERT: A 812 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7599 (ttt) REVERT: A 832 ASP cc_start: 0.6169 (t0) cc_final: 0.5833 (t0) REVERT: A 950 ASN cc_start: 0.4973 (m-40) cc_final: 0.4410 (p0) REVERT: A 1191 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7465 (mmtt) REVERT: A 1208 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6089 (mtm180) REVERT: B 214 VAL cc_start: 0.7240 (t) cc_final: 0.6968 (m) REVERT: B 215 TRP cc_start: 0.7752 (t-100) cc_final: 0.6973 (t-100) REVERT: B 292 ASN cc_start: 0.6902 (t0) cc_final: 0.6678 (t0) REVERT: B 297 GLN cc_start: 0.7949 (tt0) cc_final: 0.7727 (tt0) REVERT: B 379 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6302 (mp0) REVERT: B 440 MET cc_start: 0.8418 (ttm) cc_final: 0.8138 (ttt) REVERT: C 47 CYS cc_start: 0.6352 (m) cc_final: 0.6005 (m) REVERT: C 119 PHE cc_start: 0.6954 (m-80) cc_final: 0.6713 (m-80) REVERT: C 210 GLU cc_start: 0.7302 (tt0) cc_final: 0.6548 (tm-30) REVERT: C 355 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7869 (mp) REVERT: C 370 ARG cc_start: 0.7187 (ttm170) cc_final: 0.6737 (mmm-85) outliers start: 37 outliers final: 21 residues processed: 180 average time/residue: 0.3669 time to fit residues: 75.5984 Evaluate side-chains 175 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 92 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 134 optimal weight: 0.0870 chunk 150 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.165398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.126390 restraints weight = 19258.918| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 3.08 r_work: 0.3685 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14612 Z= 0.161 Angle : 0.564 9.473 19985 Z= 0.294 Chirality : 0.042 0.231 2176 Planarity : 0.005 0.055 2427 Dihedral : 14.303 145.752 2253 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.41 % Allowed : 16.18 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.21), residues: 1652 helix: 0.89 (0.19), residues: 706 sheet: 0.10 (0.35), residues: 231 loop : -0.09 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 617 TYR 0.030 0.002 TYR A 479 PHE 0.022 0.002 PHE B 119 TRP 0.025 0.001 TRP C 278 HIS 0.007 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (14612) covalent geometry : angle 0.56414 / 0.29 (19985) hydrogen bonds : bond 0.03908 / 2.59 ( 682) hydrogen bonds : angle 5.07964 / 3.60 ( 1878) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.518 Fit side-chains REVERT: A 229 VAL cc_start: 0.8038 (t) cc_final: 0.7802 (m) REVERT: A 288 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7045 (mtm180) REVERT: A 413 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7356 (tt) REVERT: A 812 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7582 (ttt) REVERT: A 832 ASP cc_start: 0.6125 (t0) cc_final: 0.5753 (t0) REVERT: A 950 ASN cc_start: 0.4975 (m-40) cc_final: 0.4439 (p0) REVERT: A 1191 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7469 (mmtt) REVERT: B 214 VAL cc_start: 0.7250 (t) cc_final: 0.6976 (m) REVERT: B 215 TRP cc_start: 0.7765 (t-100) cc_final: 0.6990 (t-100) REVERT: B 292 ASN cc_start: 0.6922 (t0) cc_final: 0.6691 (t0) REVERT: B 297 GLN cc_start: 0.7927 (tt0) cc_final: 0.7707 (tt0) REVERT: B 379 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6298 (mp0) REVERT: B 440 MET cc_start: 0.8437 (ttm) cc_final: 0.8176 (ttt) REVERT: C 47 CYS cc_start: 0.6346 (m) cc_final: 0.6012 (m) REVERT: C 119 PHE cc_start: 0.6938 (m-80) cc_final: 0.6702 (m-80) REVERT: C 210 GLU cc_start: 0.7365 (tt0) cc_final: 0.6541 (tm-30) REVERT: C 355 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7865 (mp) REVERT: C 370 ARG cc_start: 0.7215 (ttm170) cc_final: 0.6762 (mmm-85) REVERT: C 400 GLU cc_start: 0.8894 (tt0) cc_final: 0.8616 (pm20) REVERT: C 439 MET cc_start: 0.7351 (tpp) cc_final: 0.6897 (mpp) outliers start: 35 outliers final: 21 residues processed: 169 average time/residue: 0.3449 time to fit residues: 67.2432 Evaluate side-chains 170 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 146 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 88 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.166748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.128171 restraints weight = 19168.547| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.01 r_work: 0.3706 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14612 Z= 0.138 Angle : 0.548 9.235 19985 Z= 0.286 Chirality : 0.042 0.205 2176 Planarity : 0.005 0.048 2427 Dihedral : 14.269 145.876 2253 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.00 % Allowed : 16.87 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.21), residues: 1652 helix: 0.96 (0.20), residues: 706 sheet: 0.14 (0.35), residues: 231 loop : -0.04 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 617 TYR 0.029 0.001 TYR A 479 PHE 0.021 0.001 PHE B 119 TRP 0.031 0.001 TRP C 278 HIS 0.006 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14612) covalent geometry : angle 0.54846 / 0.29 (19985) hydrogen bonds : bond 0.03742 / 2.49 ( 682) hydrogen bonds : angle 5.00176 / 3.55 ( 1878) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3304 Ramachandran restraints generated. 1652 Oldfield, 0 Emsley, 1652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.508 Fit side-chains REVERT: A 229 VAL cc_start: 0.8007 (t) cc_final: 0.7759 (m) REVERT: A 288 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.7019 (mtm180) REVERT: A 413 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7366 (tt) REVERT: A 812 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7522 (ttt) REVERT: A 832 ASP cc_start: 0.6048 (t0) cc_final: 0.5733 (t0) REVERT: A 950 ASN cc_start: 0.4968 (m-40) cc_final: 0.4450 (p0) REVERT: A 1191 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7530 (mmtt) REVERT: A 1208 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6048 (mtm180) REVERT: B 214 VAL cc_start: 0.7170 (t) cc_final: 0.6913 (m) REVERT: B 215 TRP cc_start: 0.7751 (t-100) cc_final: 0.6979 (t-100) REVERT: B 292 ASN cc_start: 0.6914 (t0) cc_final: 0.6650 (t0) REVERT: B 297 GLN cc_start: 0.7927 (tt0) cc_final: 0.7708 (tt0) REVERT: B 379 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6283 (mp0) REVERT: B 440 MET cc_start: 0.8406 (ttm) cc_final: 0.8147 (ttt) REVERT: C 47 CYS cc_start: 0.6252 (m) cc_final: 0.5918 (m) REVERT: C 119 PHE cc_start: 0.6938 (m-80) cc_final: 0.6691 (m-80) REVERT: C 210 GLU cc_start: 0.7267 (tt0) cc_final: 0.6555 (tm-30) REVERT: C 370 ARG cc_start: 0.7178 (ttm170) cc_final: 0.6729 (mmm-85) REVERT: C 400 GLU cc_start: 0.8896 (tt0) cc_final: 0.8616 (pm20) REVERT: C 439 MET cc_start: 0.7313 (tpp) cc_final: 0.6894 (mpp) outliers start: 29 outliers final: 19 residues processed: 165 average time/residue: 0.3720 time to fit residues: 70.1860 Evaluate side-chains 168 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 812 MET Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 66 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 6 optimal weight: 0.0370 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.167026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.127441 restraints weight = 19142.448| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.91 r_work: 0.3724 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14612 Z= 0.137 Angle : 0.554 10.449 19985 Z= 0.287 Chirality : 0.042 0.210 2176 Planarity : 0.005 0.050 2427 Dihedral : 14.264 145.915 2253 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.34 % Allowed : 16.39 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.21), residues: 1652 helix: 0.97 (0.20), residues: 707 sheet: 0.14 (0.35), residues: 231 loop : -0.04 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 233 TYR 0.028 0.001 TYR A 479 PHE 0.020 0.001 PHE A1092 TRP 0.027 0.001 TRP C 278 HIS 0.007 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (14612) covalent geometry : angle 0.55380 / 0.29 (19985) hydrogen bonds : bond 0.03700 / 2.46 ( 682) hydrogen bonds : angle 4.97016 / 3.53 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3779.53 seconds wall clock time: 65 minutes 11.91 seconds (3911.91 seconds total)