Starting phenix.real_space_refine on Thu Sep 18 04:53:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ic1_52824/09_2025/9ic1_52824.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ic1_52824/09_2025/9ic1_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_52824/09_2025/9ic1_52824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ic1_52824/09_2025/9ic1_52824.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ic1_52824/09_2025/9ic1_52824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ic1_52824/09_2025/9ic1_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-2.0-5805/lib/python3.9/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, 29 Unusual residues: {' CA': 1, 'DCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.83, per 1000 atoms: 0.27 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: 1.18 Conformation dependent library (CDL) restraints added in 468.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.82 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: 2.59 Time building geometry restraints manager: 1.47 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=" C6 DCP A1302 " pdb=" N1 DCP A1302 " ideal model delta sigma weight residual 1.375 1.335 0.040 1.20e-02 6.94e+03 1.11e+01 bond pdb=" C4 DCP A1302 " pdb=" C5 DCP A1302 " ideal model delta sigma weight residual 1.426 1.387 0.039 1.20e-02 6.94e+03 1.05e+01 bond pdb=" O1A DCP A1302 " pdb=" PA DCP A1302 " ideal model delta sigma weight residual 1.477 1.509 -0.032 1.00e-02 1.00e+04 1.01e+01 bond pdb=" O1B DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 1.477 1.510 -0.033 1.10e-02 8.26e+03 9.24e+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 - 3.96: 19968 3.96 - 7.92: 14 7.92 - 11.88: 1 11.88 - 15.85: 1 15.85 - 19.81: 1 Bond angle restraints: 19985 Sorted by residual: angle pdb=" PB DCP A1302 " pdb=" O3B DCP A1302 " pdb=" PG DCP A1302 " ideal model delta sigma weight residual 139.87 120.06 19.81 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PA DCP A1302 " pdb=" O3A DCP A1302 " pdb=" PB DCP A1302 " ideal model delta sigma weight residual 136.83 121.04 15.79 1.00e+00 1.00e+00 2.49e+02 angle pdb=" O1G DCP A1302 " pdb=" PG DCP A1302 " pdb=" O3B DCP A1302 " ideal model delta sigma weight residual 110.47 103.72 6.75 1.64e+00 3.70e-01 1.69e+01 angle pdb=" C2' DCP A1302 " pdb=" C1' DCP A1302 " pdb=" N1 DCP A1302 " ideal model delta sigma weight residual 113.92 109.39 4.53 1.28e+00 6.12e-01 1.26e+01 angle pdb=" N VAL A 378 " pdb=" CA VAL A 378 " pdb=" C VAL A 378 " ideal model delta sigma weight residual 112.96 109.48 3.48 1.00e+00 1.00e+00 1.21e+01 ... (remaining 19980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.56: 8338 28.56 - 57.12: 252 57.12 - 85.68: 15 85.68 - 114.24: 0 114.24 - 142.80: 2 Dihedral angle restraints: 8607 sinusoidal: 3759 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 8604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1571 0.036 - 0.071: 445 0.071 - 0.107: 128 0.107 - 0.143: 29 0.143 - 0.178: 3 Chirality restraints: 2176 Sorted by residual: 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 chirality pdb=" CA ILE A1185 " pdb=" N ILE A1185 " pdb=" C ILE A1185 " pdb=" CB ILE A1185 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-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 2.510 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 2.510 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.350 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 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 0.043 14612 Z= 0.157 Angle : 0.555 19.807 19985 Z= 0.361 Chirality : 0.038 0.178 2176 Planarity : 0.004 0.046 2427 Dihedral : 12.844 142.799 5473 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 aren 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 covalent geometry : bond 0.00278 (14612) covalent geometry : angle 0.55502 (19985) hydrogen bonds : bond 0.17060 ( 682) hydrogen bonds : angle 6.85903 ( 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 : 0.495 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: 0.6550 (tm-30) outliers start: 9 outliers final: 5 residues processed: 279 average time/residue: 0.5534 time to fit residues: 170.6318 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 : 0.446 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4478 r_free = 0.4478 target = 0.171085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.131520 restraints weight = 19421.911| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 3.00 r_work: 0.3898 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14612 Z= 0.258 Angle : 0.649 11.019 19985 Z= 0.338 Chirality : 0.046 0.207 2176 Planarity : 0.005 0.050 2427 Dihedral : 14.484 146.109 2253 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.17 % Allowed : 10.33 % Favored : 86.50 % 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 aren not related in a simple way. whole: 0.54 (0.20), residues: 1652 helix: 0.86 (0.19), residues: 703 sheet: 0.34 (0.34), residues: 228 loop : 0.02 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 617 TYR 0.014 0.002 TYR A 150 PHE 0.017 0.002 PHE A1092 TRP 0.014 0.002 TRP A 220 HIS 0.009 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00602 (14612) covalent geometry : angle 0.64924 (19985) hydrogen bonds : bond 0.04862 ( 682) hydrogen bonds : angle 5.50970 ( 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 219 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.564 Fit side-chains REVERT: A 137 GLN cc_start: 0.6335 (OUTLIER) cc_final: 0.5286 (mp10) REVERT: A 288 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6887 (mtm180) REVERT: A 354 ASN cc_start: 0.7832 (OUTLIER) cc_final: 0.7548 (m110) REVERT: A 469 ASP cc_start: 0.7565 (t0) cc_final: 0.7342 (t0) REVERT: A 541 GLN cc_start: 0.5065 (mm-40) cc_final: 0.4831 (mm-40) REVERT: A 832 ASP cc_start: 0.5913 (t0) cc_final: 0.5561 (t0) REVERT: A 950 ASN cc_start: 0.4884 (m-40) cc_final: 0.4374 (p0) REVERT: B 100 PHE cc_start: 0.7247 (m-80) cc_final: 0.7033 (m-80) REVERT: B 215 TRP cc_start: 0.7752 (t-100) cc_final: 0.6949 (t-100) REVERT: B 249 SER cc_start: 0.7792 (p) cc_final: 0.7573 (t) REVERT: B 379 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6247 (mp0) REVERT: B 401 GLN cc_start: 0.6922 (mt0) cc_final: 0.6708 (mt0) REVERT: C 47 CYS cc_start: 0.6068 (m) cc_final: 0.5664 (m) REVERT: C 107 GLN cc_start: 0.7101 (pt0) cc_final: 0.6512 (pm20) REVERT: C 119 PHE cc_start: 0.6841 (m-80) cc_final: 0.6578 (m-80) REVERT: C 169 ASN cc_start: 0.6200 (m-40) cc_final: 0.5775 (p0) REVERT: C 355 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7813 (mp) REVERT: C 366 THR cc_start: 0.6933 (m) cc_final: 0.6621 (p) REVERT: C 370 ARG cc_start: 0.7035 (ttm170) cc_final: 0.6546 (mmm-85) REVERT: C 428 GLN cc_start: 0.6075 (tt0) cc_final: 0.5167 (tm-30) outliers start: 46 outliers final: 19 residues processed: 198 average time/residue: 0.4466 time to fit residues: 100.1304 Evaluate side-chains 180 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 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 1140 LEU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1189 LEU 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 92 MET Chi-restraints excluded: chain C residue 103 ASP 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 108 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 160 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN 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 = 0.4517 r_free = 0.4517 target = 0.174703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.135290 restraints weight = 19373.418| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 3.02 r_work: 0.3944 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14612 Z= 0.139 Angle : 0.537 8.111 19985 Z= 0.279 Chirality : 0.041 0.159 2176 Planarity : 0.005 0.049 2427 Dihedral : 14.169 145.403 2246 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.62 % Allowed : 12.26 % Favored : 85.12 % 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 aren not related in a simple way. whole: 0.66 (0.20), residues: 1652 helix: 0.99 (0.19), residues: 715 sheet: 0.28 (0.34), residues: 233 loop : 0.07 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 617 TYR 0.012 0.001 TYR A 150 PHE 0.011 0.001 PHE A1092 TRP 0.011 0.001 TRP C 278 HIS 0.005 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00311 (14612) covalent geometry : angle 0.53703 (19985) hydrogen bonds : bond 0.03859 ( 682) hydrogen bonds : angle 5.13820 ( 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 211 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.647 Fit side-chains REVERT: A 137 GLN cc_start: 0.6248 (OUTLIER) cc_final: 0.5206 (mp10) REVERT: A 288 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6856 (mtm180) REVERT: A 354 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7576 (m110) REVERT: A 399 ASP cc_start: 0.6764 (OUTLIER) cc_final: 0.6476 (t0) REVERT: A 823 ARG cc_start: 0.6936 (mmm-85) cc_final: 0.6589 (mmt180) REVERT: A 832 ASP cc_start: 0.5788 (t0) cc_final: 0.5444 (t0) REVERT: A 950 ASN cc_start: 0.4761 (m-40) cc_final: 0.4293 (p0) REVERT: A 1208 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.5899 (mtm180) REVERT: A 1223 ILE cc_start: 0.6692 (OUTLIER) cc_final: 0.6025 (pt) REVERT: B 92 MET cc_start: 0.7000 (tpt) cc_final: 0.6788 (mmt) REVERT: B 214 VAL cc_start: 0.6928 (t) cc_final: 0.6667 (m) REVERT: B 215 TRP cc_start: 0.7648 (t-100) cc_final: 0.6917 (t-100) REVERT: B 379 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6203 (mp0) REVERT: C 47 CYS cc_start: 0.5967 (m) cc_final: 0.5593 (m) REVERT: C 107 GLN cc_start: 0.7041 (pt0) cc_final: 0.6446 (pm20) REVERT: C 119 PHE cc_start: 0.6780 (m-80) cc_final: 0.6496 (m-80) REVERT: C 169 ASN cc_start: 0.6306 (m-40) cc_final: 0.6025 (OUTLIER) REVERT: C 370 ARG cc_start: 0.6950 (ttm170) cc_final: 0.6498 (mmm-85) REVERT: C 428 GLN cc_start: 0.5890 (tt0) cc_final: 0.5017 (tm-30) outliers start: 38 outliers final: 12 residues processed: 192 average time/residue: 0.4841 time to fit residues: 104.7312 Evaluate side-chains 169 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 399 ASP Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 794 ILE 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 A residue 1223 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 434 THR Chi-restraints excluded: chain C residue 251 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 37 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A1202 ASN ** 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 = 0.4320 r_free = 0.4320 target = 0.165643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.126339 restraints weight = 19214.706| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.88 r_work: 0.3706 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14612 Z= 0.150 Angle : 0.534 7.302 19985 Z= 0.277 Chirality : 0.041 0.159 2176 Planarity : 0.004 0.048 2427 Dihedral : 14.095 145.738 2246 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.48 % Allowed : 13.29 % Favored : 84.23 % 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 aren not related in a simple way. whole: 0.65 (0.20), residues: 1652 helix: 1.01 (0.19), residues: 716 sheet: 0.23 (0.34), residues: 231 loop : 0.04 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 597 TYR 0.013 0.001 TYR A 150 PHE 0.024 0.001 PHE A 766 TRP 0.013 0.001 TRP C 278 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00344 (14612) covalent geometry : angle 0.53446 (19985) hydrogen bonds : bond 0.03748 ( 682) hydrogen bonds : angle 5.02101 ( 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 194 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 288 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7082 (mtm180) REVERT: A 354 ASN cc_start: 0.7945 (OUTLIER) cc_final: 0.7662 (m110) REVERT: A 399 ASP cc_start: 0.7045 (t0) cc_final: 0.6782 (t0) REVERT: A 541 GLN cc_start: 0.5115 (mm-40) cc_final: 0.4905 (mm-40) REVERT: A 812 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7526 (ttt) REVERT: A 823 ARG cc_start: 0.7166 (mmm-85) cc_final: 0.6841 (mmt180) REVERT: A 950 ASN cc_start: 0.5000 (m-40) cc_final: 0.4491 (p0) REVERT: A 1208 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6108 (mtm180) REVERT: A 1223 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6212 (pt) REVERT: B 92 MET cc_start: 0.7202 (tpt) cc_final: 0.7002 (mmt) REVERT: B 214 VAL cc_start: 0.7167 (t) cc_final: 0.6906 (m) REVERT: B 215 TRP cc_start: 0.7782 (t-100) cc_final: 0.7064 (t-100) REVERT: B 379 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: C 47 CYS cc_start: 0.6226 (m) cc_final: 0.5838 (m) REVERT: C 107 GLN cc_start: 0.7301 (pt0) cc_final: 0.6724 (pm20) REVERT: C 119 PHE cc_start: 0.6936 (m-80) cc_final: 0.6642 (m-80) REVERT: C 210 GLU cc_start: 0.7308 (tt0) cc_final: 0.6627 (tm-30) REVERT: C 370 ARG cc_start: 0.7198 (ttm170) cc_final: 0.6747 (mmm-85) REVERT: C 428 GLN cc_start: 0.6145 (tt0) cc_final: 0.5311 (tm-30) outliers start: 36 outliers final: 13 residues processed: 176 average time/residue: 0.4923 time to fit residues: 97.5574 Evaluate side-chains 170 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU 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 812 MET Chi-restraints excluded: chain A residue 1131 ILE Chi-restraints excluded: chain A residue 1189 LEU Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain A residue 1223 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 103 ASP Chi-restraints excluded: chain C residue 212 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.164697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.125478 restraints weight = 19222.536| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.88 r_work: 0.3704 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2179 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= 0.160 Angle : 0.536 8.668 19985 Z= 0.277 Chirality : 0.042 0.169 2176 Planarity : 0.005 0.047 2427 Dihedral : 14.105 145.694 2246 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.10 % Allowed : 13.91 % Favored : 82.99 % 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 aren not related in a simple way. whole: 0.64 (0.20), residues: 1652 helix: 1.07 (0.19), residues: 712 sheet: 0.26 (0.34), residues: 233 loop : -0.05 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 546 TYR 0.014 0.001 TYR A 150 PHE 0.019 0.001 PHE A 766 TRP 0.016 0.001 TRP C 278 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00370 (14612) covalent geometry : angle 0.53619 (19985) hydrogen bonds : bond 0.03757 ( 682) hydrogen bonds : angle 4.96647 ( 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 201 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 137 GLN cc_start: 0.6605 (OUTLIER) cc_final: 0.5541 (mp10) REVERT: A 288 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7079 (mtm180) REVERT: A 399 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6749 (t0) REVERT: A 812 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7531 (ttt) REVERT: A 950 ASN cc_start: 0.5036 (m-40) cc_final: 0.4547 (p0) REVERT: A 1208 ARG cc_start: 0.6791 (OUTLIER) cc_final: 0.6079 (mtm180) REVERT: B 92 MET cc_start: 0.7265 (tpt) cc_final: 0.7058 (mmt) REVERT: B 214 VAL cc_start: 0.7131 (t) cc_final: 0.6864 (m) REVERT: B 215 TRP cc_start: 0.7739 (t-100) cc_final: 0.6997 (t-100) REVERT: B 292 ASN cc_start: 0.6328 (t0) cc_final: 0.6060 (t0) REVERT: B 379 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: C 47 CYS cc_start: 0.6232 (m) cc_final: 0.5851 (m) REVERT: C 119 PHE cc_start: 0.6923 (m-80) cc_final: 0.6656 (m-80) REVERT: C 210 GLU cc_start: 0.7322 (tt0) cc_final: 0.6593 (tm-30) REVERT: C 215 TRP cc_start: 0.7307 (t-100) cc_final: 0.6976 (t-100) REVERT: C 242 MET cc_start: 0.4899 (ttp) cc_final: 0.3970 (mpm) REVERT: C 355 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7812 (mp) REVERT: C 370 ARG cc_start: 0.7219 (ttm170) cc_final: 0.6743 (mmm-85) outliers start: 45 outliers final: 17 residues processed: 183 average time/residue: 0.4976 time to fit residues: 102.1592 Evaluate side-chains 173 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 399 ASP Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 812 MET 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 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 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 316 VAL Chi-restraints excluded: chain C residue 355 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 162 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 152 optimal weight: 30.0000 chunk 153 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4296 r_free = 0.4296 target = 0.163674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.124361 restraints weight = 19285.351| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.87 r_work: 0.3689 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14612 Z= 0.194 Angle : 0.565 7.945 19985 Z= 0.291 Chirality : 0.043 0.178 2176 Planarity : 0.005 0.048 2427 Dihedral : 14.158 145.563 2246 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.03 % Allowed : 14.12 % 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 aren not related in a simple way. whole: 0.48 (0.20), residues: 1652 helix: 0.96 (0.19), residues: 707 sheet: 0.14 (0.34), residues: 235 loop : -0.15 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 546 TYR 0.015 0.002 TYR A 479 PHE 0.021 0.002 PHE A 766 TRP 0.018 0.001 TRP C 278 HIS 0.007 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00454 (14612) covalent geometry : angle 0.56536 (19985) hydrogen bonds : bond 0.03934 ( 682) hydrogen bonds : angle 5.04894 ( 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 195 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 137 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.5591 (mp10) REVERT: A 288 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6991 (mtm180) REVERT: A 399 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6795 (t0) REVERT: A 541 GLN cc_start: 0.5059 (mm-40) cc_final: 0.4840 (mm-40) REVERT: A 812 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7567 (ttt) REVERT: A 832 ASP cc_start: 0.6112 (t0) cc_final: 0.5763 (t0) REVERT: A 950 ASN cc_start: 0.5160 (m-40) cc_final: 0.4454 (p0) REVERT: A 1191 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7407 (mmtt) REVERT: A 1208 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6045 (mtm180) REVERT: B 214 VAL cc_start: 0.7234 (t) cc_final: 0.6957 (m) REVERT: B 215 TRP cc_start: 0.7755 (t-100) cc_final: 0.6987 (t-100) REVERT: B 292 ASN cc_start: 0.6636 (t0) cc_final: 0.6393 (t0) REVERT: B 379 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6322 (mp0) REVERT: B 440 MET cc_start: 0.8356 (ttm) cc_final: 0.8142 (ttt) REVERT: C 47 CYS cc_start: 0.6330 (m) cc_final: 0.5979 (m) REVERT: C 210 GLU cc_start: 0.7310 (tt0) cc_final: 0.6575 (tm-30) REVERT: C 215 TRP cc_start: 0.7372 (t-100) cc_final: 0.7045 (t-100) REVERT: C 242 MET cc_start: 0.4930 (ttp) cc_final: 0.3984 (mpm) REVERT: C 355 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7847 (mp) REVERT: C 366 THR cc_start: 0.7245 (m) cc_final: 0.6890 (p) REVERT: C 370 ARG cc_start: 0.7210 (ttm170) cc_final: 0.6691 (mmm-85) REVERT: C 440 MET cc_start: 0.7824 (ttp) cc_final: 0.7567 (ttt) outliers start: 44 outliers final: 19 residues processed: 181 average time/residue: 0.4742 time to fit residues: 96.7853 Evaluate side-chains 171 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 148 LEU 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 399 ASP 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 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 103 ASP Chi-restraints excluded: chain C residue 212 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 159 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 160 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 0.0970 chunk 84 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4339 r_free = 0.4339 target = 0.167662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.128136 restraints weight = 19090.212| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.91 r_work: 0.3733 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14612 Z= 0.118 Angle : 0.519 9.318 19985 Z= 0.266 Chirality : 0.040 0.185 2176 Planarity : 0.004 0.047 2427 Dihedral : 14.104 145.838 2246 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.48 % Allowed : 15.08 % Favored : 82.44 % 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 aren not related in a simple way. whole: 0.76 (0.21), residues: 1652 helix: 1.22 (0.20), residues: 701 sheet: 0.17 (0.33), residues: 239 loop : 0.02 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 617 TYR 0.028 0.001 TYR A 479 PHE 0.019 0.001 PHE B 119 TRP 0.020 0.001 TRP C 278 HIS 0.005 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00264 (14612) covalent geometry : angle 0.51858 (19985) hydrogen bonds : bond 0.03380 ( 682) hydrogen bonds : angle 4.85554 ( 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 194 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.515 Fit side-chains REVERT: A 229 VAL cc_start: 0.8045 (t) cc_final: 0.7801 (m) REVERT: A 288 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6982 (mtm180) REVERT: A 354 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7485 (m110) REVERT: A 399 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6720 (t0) REVERT: A 447 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7481 (mt-10) REVERT: A 812 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7379 (ttt) REVERT: A 950 ASN cc_start: 0.4943 (m-40) cc_final: 0.4558 (p0) REVERT: A 1191 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7441 (mmtt) REVERT: A 1223 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6137 (pt) REVERT: B 214 VAL cc_start: 0.7181 (t) cc_final: 0.6887 (m) REVERT: B 215 TRP cc_start: 0.7706 (t-100) cc_final: 0.7011 (t-100) REVERT: B 292 ASN cc_start: 0.6695 (t0) cc_final: 0.6450 (t0) REVERT: B 379 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6360 (mp0) REVERT: B 440 MET cc_start: 0.8352 (ttm) cc_final: 0.8148 (ttt) REVERT: C 47 CYS cc_start: 0.6197 (m) cc_final: 0.5802 (m) REVERT: C 119 PHE cc_start: 0.7124 (m-80) cc_final: 0.6886 (m-80) REVERT: C 166 HIS cc_start: 0.6353 (m-70) cc_final: 0.5609 (m-70) REVERT: C 210 GLU cc_start: 0.7268 (tt0) cc_final: 0.6560 (tm-30) REVERT: C 215 TRP cc_start: 0.7372 (t-100) cc_final: 0.6988 (t-100) REVERT: C 370 ARG cc_start: 0.7134 (ttm170) cc_final: 0.6655 (mmm-85) REVERT: C 400 GLU cc_start: 0.8914 (tt0) cc_final: 0.8625 (pm20) REVERT: C 439 MET cc_start: 0.7329 (mpp) cc_final: 0.6898 (mpp) outliers start: 36 outliers final: 19 residues processed: 179 average time/residue: 0.3946 time to fit residues: 81.0995 Evaluate side-chains 175 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 399 ASP 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 1189 LEU Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1223 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 426 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 34 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.163827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.124393 restraints weight = 19296.534| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 3.14 r_work: 0.3667 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14612 Z= 0.216 Angle : 0.593 8.885 19985 Z= 0.303 Chirality : 0.044 0.193 2176 Planarity : 0.005 0.047 2427 Dihedral : 14.268 145.529 2246 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.96 % Allowed : 15.56 % Favored : 81.47 % 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 aren not related in a simple way. whole: 0.50 (0.21), residues: 1652 helix: 1.04 (0.20), residues: 695 sheet: 0.06 (0.33), residues: 237 loop : -0.15 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 617 TYR 0.019 0.002 TYR A 479 PHE 0.022 0.002 PHE A 766 TRP 0.026 0.001 TRP C 278 HIS 0.007 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00505 (14612) covalent geometry : angle 0.59266 (19985) hydrogen bonds : bond 0.04012 ( 682) hydrogen bonds : angle 5.06589 ( 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 191 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.543 Fit side-chains REVERT: A 137 GLN cc_start: 0.6744 (OUTLIER) cc_final: 0.5626 (mp10) REVERT: A 288 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7070 (mtm180) REVERT: A 399 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6865 (t0) REVERT: A 812 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7562 (ttt) REVERT: A 832 ASP cc_start: 0.6184 (t0) cc_final: 0.5857 (t0) REVERT: A 950 ASN cc_start: 0.5091 (m-40) cc_final: 0.4550 (p0) REVERT: A 1191 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7542 (mppt) REVERT: A 1223 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6073 (pt) REVERT: B 214 VAL cc_start: 0.7243 (t) cc_final: 0.6900 (m) REVERT: B 215 TRP cc_start: 0.7732 (t-100) cc_final: 0.7015 (t-100) REVERT: B 292 ASN cc_start: 0.6951 (t0) cc_final: 0.6704 (t0) REVERT: B 379 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.6354 (mp0) REVERT: C 47 CYS cc_start: 0.6423 (m) cc_final: 0.6037 (m) REVERT: C 119 PHE cc_start: 0.7102 (m-80) cc_final: 0.6875 (m-80) REVERT: C 210 GLU cc_start: 0.7356 (tt0) cc_final: 0.6710 (tm-30) REVERT: C 215 TRP cc_start: 0.7476 (t-100) cc_final: 0.7133 (t-100) REVERT: C 355 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7892 (mp) REVERT: C 370 ARG cc_start: 0.7227 (ttm170) cc_final: 0.6735 (mmm-85) REVERT: C 400 GLU cc_start: 0.8909 (tt0) cc_final: 0.8624 (pm20) outliers start: 43 outliers final: 23 residues processed: 176 average time/residue: 0.3806 time to fit residues: 76.7046 Evaluate side-chains 174 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 215 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 399 ASP 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 1189 LEU Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1223 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 426 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 92 optimal weight: 3.9990 chunk 152 optimal weight: 0.0070 chunk 29 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.166899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.127269 restraints weight = 19208.810| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.92 r_work: 0.3726 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2528 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= 0.134 Angle : 0.549 9.069 19985 Z= 0.279 Chirality : 0.041 0.185 2176 Planarity : 0.004 0.047 2427 Dihedral : 14.218 145.717 2246 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.48 % Allowed : 16.32 % Favored : 81.20 % 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 aren not related in a simple way. whole: 0.65 (0.21), residues: 1652 helix: 1.10 (0.20), residues: 701 sheet: 0.11 (0.34), residues: 230 loop : -0.00 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 233 TYR 0.029 0.001 TYR A 479 PHE 0.019 0.001 PHE B 119 TRP 0.031 0.001 TRP C 278 HIS 0.007 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00305 (14612) covalent geometry : angle 0.54894 (19985) hydrogen bonds : bond 0.03495 ( 682) hydrogen bonds : angle 4.92175 ( 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 190 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.553 Fit side-chains REVERT: A 229 VAL cc_start: 0.7989 (t) cc_final: 0.7757 (m) REVERT: A 288 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6991 (mtm180) REVERT: A 399 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6737 (t0) REVERT: A 413 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7293 (tt) REVERT: A 447 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7467 (mt-10) REVERT: A 812 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7441 (ttt) REVERT: A 832 ASP cc_start: 0.6107 (t0) cc_final: 0.5758 (t0) REVERT: A 950 ASN cc_start: 0.4962 (m-40) cc_final: 0.4568 (p0) REVERT: A 1191 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7464 (mmtt) REVERT: A 1208 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6079 (mtm180) REVERT: A 1223 ILE cc_start: 0.7017 (OUTLIER) cc_final: 0.6118 (pt) REVERT: B 214 VAL cc_start: 0.7204 (t) cc_final: 0.6918 (m) REVERT: B 215 TRP cc_start: 0.7686 (t-100) cc_final: 0.6958 (t-100) REVERT: B 292 ASN cc_start: 0.6981 (t0) cc_final: 0.6703 (t0) REVERT: B 379 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.6352 (mp0) REVERT: C 47 CYS cc_start: 0.6210 (m) cc_final: 0.5816 (m) REVERT: C 119 PHE cc_start: 0.7133 (m-80) cc_final: 0.6838 (m-80) REVERT: C 166 HIS cc_start: 0.6410 (m-70) cc_final: 0.5596 (m-70) REVERT: C 210 GLU cc_start: 0.7305 (tt0) cc_final: 0.6596 (tm-30) REVERT: C 215 TRP cc_start: 0.7403 (t-100) cc_final: 0.7004 (t-100) REVERT: C 370 ARG cc_start: 0.7140 (ttm170) cc_final: 0.6658 (mmm-85) REVERT: C 400 GLU cc_start: 0.8920 (tt0) cc_final: 0.8624 (pm20) outliers start: 36 outliers final: 20 residues processed: 178 average time/residue: 0.4481 time to fit residues: 90.6027 Evaluate side-chains 179 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 399 ASP 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 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 A residue 1223 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 103 ASP Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 146 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4316 r_free = 0.4316 target = 0.165358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.125433 restraints weight = 19319.050| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.92 r_work: 0.3693 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14612 Z= 0.187 Angle : 0.602 10.751 19985 Z= 0.306 Chirality : 0.043 0.195 2176 Planarity : 0.005 0.051 2427 Dihedral : 14.262 145.663 2246 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.13 % Allowed : 16.74 % 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 aren not related in a simple way. whole: 0.50 (0.21), residues: 1652 helix: 0.98 (0.20), residues: 705 sheet: 0.01 (0.34), residues: 232 loop : -0.09 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 233 TYR 0.028 0.002 TYR A 479 PHE 0.018 0.002 PHE A 766 TRP 0.035 0.001 TRP C 278 HIS 0.007 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00436 (14612) covalent geometry : angle 0.60185 (19985) hydrogen bonds : bond 0.03857 ( 682) hydrogen bonds : angle 5.01600 ( 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 179 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.572 Fit side-chains REVERT: A 229 VAL cc_start: 0.7989 (t) cc_final: 0.7755 (m) REVERT: A 288 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7045 (mtm180) REVERT: A 399 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6795 (t0) REVERT: A 447 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7435 (mt-10) REVERT: A 812 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7531 (ttt) REVERT: A 832 ASP cc_start: 0.6102 (t0) cc_final: 0.5811 (t0) REVERT: A 950 ASN cc_start: 0.5069 (m-40) cc_final: 0.4543 (p0) REVERT: A 1191 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7439 (mmtt) REVERT: A 1223 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6043 (pt) REVERT: B 214 VAL cc_start: 0.7185 (t) cc_final: 0.6893 (m) REVERT: B 215 TRP cc_start: 0.7710 (t-100) cc_final: 0.6978 (t-100) REVERT: B 292 ASN cc_start: 0.7100 (t0) cc_final: 0.6828 (t0) REVERT: B 368 GLU cc_start: 0.7055 (pm20) cc_final: 0.6840 (pm20) REVERT: B 379 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6388 (mp0) REVERT: C 47 CYS cc_start: 0.6309 (m) cc_final: 0.5943 (m) REVERT: C 119 PHE cc_start: 0.7128 (m-80) cc_final: 0.6842 (m-80) REVERT: C 210 GLU cc_start: 0.7300 (tt0) cc_final: 0.6669 (tm-30) REVERT: C 215 TRP cc_start: 0.7399 (t-100) cc_final: 0.7038 (t-100) REVERT: C 355 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7845 (mp) REVERT: C 370 ARG cc_start: 0.7212 (ttm170) cc_final: 0.6705 (mmm-85) REVERT: C 400 GLU cc_start: 0.8930 (tt0) cc_final: 0.8624 (pm20) outliers start: 31 outliers final: 19 residues processed: 166 average time/residue: 0.4475 time to fit residues: 84.0520 Evaluate side-chains 171 residues out of total 1454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 399 ASP 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 1189 LEU Chi-restraints excluded: chain A residue 1191 LYS Chi-restraints excluded: chain A residue 1223 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 103 ASP Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 434 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 66 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.0170 chunk 82 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** 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 = 0.4352 r_free = 0.4352 target = 0.168859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.129598 restraints weight = 19083.328| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.92 r_work: 0.3755 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14612 Z= 0.122 Angle : 0.570 11.780 19985 Z= 0.291 Chirality : 0.041 0.200 2176 Planarity : 0.005 0.115 2427 Dihedral : 14.177 145.848 2246 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.00 % Allowed : 16.94 % Favored : 81.06 % 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 aren not related in a simple way. whole: 0.64 (0.21), residues: 1652 helix: 1.09 (0.20), residues: 702 sheet: 0.05 (0.34), residues: 229 loop : 0.03 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 233 TYR 0.025 0.001 TYR A 479 PHE 0.020 0.001 PHE A1092 TRP 0.037 0.001 TRP C 278 HIS 0.007 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00271 (14612) covalent geometry : angle 0.57040 (19985) hydrogen bonds : bond 0.03478 ( 682) hydrogen bonds : angle 4.89027 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4437.31 seconds wall clock time: 76 minutes 35.67 seconds (4595.67 seconds total)