Starting phenix.real_space_refine on Thu Sep 18 04:24:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ic0_52823/09_2025/9ic0_52823.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ic0_52823/09_2025/9ic0_52823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ic0_52823/09_2025/9ic0_52823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ic0_52823/09_2025/9ic0_52823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ic0_52823/09_2025/9ic0_52823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ic0_52823/09_2025/9ic0_52823.map" } resolution = 3.24 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= 0.158 sd= 0.963 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 2 9.91 5 P 44 5.49 5 S 80 5.16 5 C 8771 2.51 5 N 2460 2.21 5 O 2630 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: 13987 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 942, 7500 Classifications: {'peptide': 942} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 62, 'TRANS': 879} Chain breaks: 6 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2807 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 329} Chain breaks: 4 Chain: "C" Number of atoms: 2810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2810 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 331} Chain breaks: 3 Chain: "P" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 438 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "T" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 402 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' CA': 2, 'DCP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.42, per 1000 atoms: 0.24 Number of scatterers: 13987 At special positions: 0 Unit cell: (96.048, 106.812, 137.448, 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 2 19.99 S 80 16.00 P 44 15.00 O 2630 8.00 N 2460 7.00 C 8771 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: 1.14 Conformation dependent library (CDL) restraints added in 616.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3040 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 14 sheets defined 47.9% alpha, 13.0% beta 18 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 63 through 72 removed outlier: 4.575A pdb=" N GLN A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 93 removed outlier: 3.526A pdb=" N HIS A 93 " --> pdb=" O HIS A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 142 Proline residue: A 132 - end of helix removed outlier: 3.887A pdb=" N ALA A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.904A pdb=" N ASP A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.552A pdb=" N TYR A 265 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.793A pdb=" N GLY A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 299 Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.878A pdb=" N ILE A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 370 through 397 removed outlier: 3.836A pdb=" N GLN A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 402 through 412 removed outlier: 4.193A pdb=" N LEU A 406 " --> pdb=" O HIS A 402 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 453 removed outlier: 3.690A pdb=" N ARG A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 464 removed outlier: 4.961A pdb=" N GLY A 458 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG A 460 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR A 461 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS A 462 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 532 removed outlier: 3.708A pdb=" N LEU A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 540 removed outlier: 3.731A pdb=" N ASP A 538 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.970A pdb=" N LYS A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 557 " --> pdb=" O TRP A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 Processing helix chain 'A' and resid 629 through 640 Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 748 through 754 Processing helix chain 'A' and resid 764 through 776 Processing helix chain 'A' and resid 778 through 788 removed outlier: 5.614A pdb=" N LYS A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ARG A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 871 through 886 Processing helix chain 'A' and resid 892 through 901 Processing helix chain 'A' and resid 908 through 918 Processing helix chain 'A' and resid 920 through 933 removed outlier: 3.655A pdb=" N ILE A 926 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 948 Processing helix chain 'A' and resid 952 through 965 Processing helix chain 'A' and resid 1032 through 1042 removed outlier: 3.691A pdb=" N LYS A1038 " --> pdb=" O GLU A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1067 Processing helix chain 'A' and resid 1070 through 1101 removed outlier: 3.646A pdb=" N ARG A1074 " --> pdb=" O PHE A1070 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A1079 " --> pdb=" O VAL A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1147 Processing helix chain 'A' and resid 1153 through 1157 removed outlier: 4.324A pdb=" N PHE A1157 " --> pdb=" O SER A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1188 removed outlier: 3.716A pdb=" N ARG A1187 " --> pdb=" O GLY A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1206 Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 120 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 267 removed outlier: 3.564A pdb=" N GLN B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 267 " --> pdb=" O TRP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.635A pdb=" N HIS B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.840A pdb=" N PHE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 409 removed outlier: 3.866A pdb=" N ASN B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 removed outlier: 3.784A pdb=" N GLU B 434 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N MET B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 470 through 481 Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.696A pdb=" N LEU C 86 " --> pdb=" O LYS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 197 removed outlier: 3.849A pdb=" N ALA C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.151A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.856A pdb=" N LEU C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 354 removed outlier: 3.778A pdb=" N LEU C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 409 removed outlier: 3.682A pdb=" N LEU C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.574A pdb=" N GLU C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 482 removed outlier: 3.574A pdb=" N LEU C 471 " --> pdb=" O HIS C 467 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ASP C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 482 " --> pdb=" O TYR C 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 170 removed outlier: 3.854A pdb=" N TRP A 158 " --> pdb=" O VAL A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 417 through 419 Processing sheet with id=AA3, first strand: chain 'A' and resid 716 through 717 removed outlier: 3.624A pdb=" N TYR A 717 " --> pdb=" O PHE A 727 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 727 " --> pdb=" O TYR A 717 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1105 through 1109 removed outlier: 7.303A pdb=" N GLY A1105 " --> pdb=" O ARG A1120 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ARG A1120 " --> pdb=" O GLY A1105 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE A1107 " --> pdb=" O LEU A1118 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU A1118 " --> pdb=" O PHE A1107 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A1109 " --> pdb=" O ARG A1116 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A1164 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 127 Processing sheet with id=AA7, first strand: chain 'B' and resid 133 through 134 removed outlier: 3.881A pdb=" N LYS B 134 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS B 180 " --> pdb=" O LYS B 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 279 removed outlier: 3.551A pdb=" N TYR B 290 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 301 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LYS B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 337 " --> pdb=" O TRP B 304 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU B 306 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL B 335 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AB1, first strand: chain 'B' and resid 386 through 387 removed outlier: 7.554A pdb=" N ASP B 386 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 441 " --> pdb=" O ASP B 386 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 456 " --> pdb=" O THR B 440 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 125 through 127 removed outlier: 5.819A pdb=" N PHE C 126 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR C 243 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL C 335 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU C 301 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN C 305 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYS C 285 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 212 through 215 Processing sheet with id=AB4, first strand: chain 'C' and resid 324 through 325 Processing sheet with id=AB5, first strand: chain 'C' and resid 413 through 414 removed outlier: 7.104A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2216 1.32 - 1.44: 4155 1.44 - 1.56: 7840 1.56 - 1.69: 87 1.69 - 1.81: 127 Bond restraints: 14425 Sorted by residual: bond pdb=" C4' DCP A1301 " pdb=" O4' DCP A1301 " ideal model delta sigma weight residual 1.444 1.619 -0.175 1.00e-02 1.00e+04 3.05e+02 bond pdb=" C3' DCP A1301 " pdb=" C4' DCP A1301 " ideal model delta sigma weight residual 1.527 1.343 0.184 1.10e-02 8.26e+03 2.78e+02 bond pdb=" C4 DCP A1301 " pdb=" N4 DCP A1301 " ideal model delta sigma weight residual 1.334 1.465 -0.131 1.20e-02 6.94e+03 1.19e+02 bond pdb=" C1' DCP A1301 " pdb=" O4' DCP A1301 " ideal model delta sigma weight residual 1.418 1.313 0.105 1.20e-02 6.94e+03 7.60e+01 bond pdb=" C5 DCP A1301 " pdb=" C6 DCP A1301 " ideal model delta sigma weight residual 1.345 1.501 -0.156 1.80e-02 3.09e+03 7.56e+01 ... (remaining 14420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 19665 3.36 - 6.72: 54 6.72 - 10.08: 4 10.08 - 13.44: 1 13.44 - 16.80: 1 Bond angle restraints: 19725 Sorted by residual: angle pdb=" PB DCP A1301 " pdb=" O3B DCP A1301 " pdb=" PG DCP A1301 " ideal model delta sigma weight residual 139.87 123.07 16.80 1.00e+00 1.00e+00 2.82e+02 angle pdb=" PA DCP A1301 " pdb=" O3A DCP A1301 " pdb=" PB DCP A1301 " ideal model delta sigma weight residual 136.83 123.77 13.06 1.00e+00 1.00e+00 1.71e+02 angle pdb=" O3A DCP A1301 " pdb=" PB DCP A1301 " pdb=" O3B DCP A1301 " ideal model delta sigma weight residual 101.57 109.89 -8.32 1.54e+00 4.24e-01 2.93e+01 angle pdb=" O3B DCP A1301 " pdb=" PG DCP A1301 " pdb=" O3G DCP A1301 " ideal model delta sigma weight residual 104.48 109.45 -4.97 1.14e+00 7.76e-01 1.91e+01 angle pdb=" N VAL B 383 " pdb=" CA VAL B 383 " pdb=" C VAL B 383 " ideal model delta sigma weight residual 108.12 114.38 -6.26 1.44e+00 4.82e-01 1.89e+01 ... (remaining 19720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 7680 15.99 - 31.98: 538 31.98 - 47.97: 168 47.97 - 63.96: 87 63.96 - 79.94: 4 Dihedral angle restraints: 8477 sinusoidal: 3767 harmonic: 4710 Sorted by residual: dihedral pdb=" CA ILE C 381 " pdb=" C ILE C 381 " pdb=" N LYS C 382 " pdb=" CA LYS C 382 " ideal model delta harmonic sigma weight residual 180.00 -160.52 -19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA VAL A 179 " pdb=" C VAL A 179 " pdb=" N PHE A 180 " pdb=" CA PHE A 180 " ideal model delta harmonic sigma weight residual -180.00 -160.84 -19.16 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA GLU A 164 " pdb=" C GLU A 164 " pdb=" N GLY A 165 " pdb=" CA GLY A 165 " ideal model delta harmonic sigma weight residual 180.00 163.89 16.11 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 8474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1801 0.051 - 0.101: 266 0.101 - 0.152: 47 0.152 - 0.203: 0 0.203 - 0.254: 1 Chirality restraints: 2115 Sorted by residual: chirality pdb=" C3' DCP A1301 " pdb=" C2' DCP A1301 " pdb=" C4' DCP A1301 " pdb=" O3' DCP A1301 " both_signs ideal model delta sigma weight residual False -2.68 -2.42 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE C 381 " pdb=" CA ILE C 381 " pdb=" CG1 ILE C 381 " pdb=" CG2 ILE C 381 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE A1163 " pdb=" N ILE A1163 " pdb=" C ILE A1163 " pdb=" CB ILE A1163 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 2112 not shown) Planarity restraints: 2389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A1065 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.67e+00 pdb=" C VAL A1065 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL A1065 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A1066 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 116 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C THR B 116 " 0.025 2.00e-02 2.50e+03 pdb=" O THR B 116 " -0.009 2.00e-02 2.50e+03 pdb=" N SER B 117 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 742 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO A 743 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 743 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 743 " -0.018 5.00e-02 4.00e+02 ... (remaining 2386 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3757 2.81 - 3.33: 13147 3.33 - 3.85: 23328 3.85 - 4.38: 27390 4.38 - 4.90: 46149 Nonbonded interactions: 113771 Sorted by model distance: nonbonded pdb=" OD2 ASP A1113 " pdb="CA CA A1300 " model vdw 2.287 2.510 nonbonded pdb=" OG SER A 285 " pdb=" OH TYR A 345 " model vdw 2.297 3.040 nonbonded pdb=" OE1 GLU C 236 " pdb=" ND2 ASN C 339 " model vdw 2.300 3.120 nonbonded pdb="CA CA A1300 " pdb=" O1B DCP A1301 " model vdw 2.305 2.510 nonbonded pdb=" O PRO A 132 " pdb=" NH2 ARG A 176 " model vdw 2.306 3.120 ... (remaining 113766 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 67 through 134 or resid 179 through 482)) selection = (chain 'C' and (resid 67 through 218 or resid 231 through 388 or resid 391 throu \ gh 482)) } 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: 2.370 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.780 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 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 : 0.005 0.184 14425 Z= 0.344 Angle : 0.558 16.803 19725 Z= 0.345 Chirality : 0.038 0.254 2115 Planarity : 0.004 0.032 2389 Dihedral : 13.449 79.945 5437 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.56 % Allowed : 4.86 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.36 (0.22), residues: 1604 helix: 0.98 (0.21), residues: 640 sheet: -0.77 (0.34), residues: 231 loop : 0.07 (0.25), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 369 TYR 0.010 0.001 TYR A1086 PHE 0.015 0.001 PHE C 254 TRP 0.009 0.001 TRP A 875 HIS 0.002 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00471 (14425) covalent geometry : angle 0.55816 (19725) hydrogen bonds : bond 0.18340 ( 635) hydrogen bonds : angle 6.98403 ( 1750) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 260 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 ASP cc_start: 0.7344 (p0) cc_final: 0.7073 (p0) REVERT: A 888 MET cc_start: 0.6959 (ptp) cc_final: 0.6551 (ptt) REVERT: A 1035 MET cc_start: 0.6513 (tmm) cc_final: 0.6151 (tmm) REVERT: A 1066 VAL cc_start: 0.8785 (m) cc_final: 0.8558 (p) REVERT: B 437 ILE cc_start: 0.6078 (mt) cc_final: 0.5830 (mt) REVERT: C 437 ILE cc_start: 0.6874 (mt) cc_final: 0.6651 (mt) outliers start: 8 outliers final: 8 residues processed: 267 average time/residue: 0.1187 time to fit residues: 46.4870 Evaluate side-chains 196 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 188 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 ASP Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 332 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.0060 chunk 149 optimal weight: 3.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 ASN B 400 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.124182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.100030 restraints weight = 29436.703| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.87 r_work: 0.3521 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14425 Z= 0.223 Angle : 0.624 8.049 19725 Z= 0.319 Chirality : 0.042 0.176 2115 Planarity : 0.005 0.039 2389 Dihedral : 14.664 60.263 2244 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.76 % Allowed : 11.26 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.31 (0.21), residues: 1604 helix: 1.03 (0.20), residues: 646 sheet: -0.82 (0.34), residues: 232 loop : -0.04 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 805 TYR 0.016 0.002 TYR C 193 PHE 0.022 0.002 PHE C 254 TRP 0.013 0.002 TRP A 329 HIS 0.008 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00514 (14425) covalent geometry : angle 0.62431 (19725) hydrogen bonds : bond 0.04426 ( 635) hydrogen bonds : angle 5.44068 ( 1750) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 ASP cc_start: 0.8614 (m-30) cc_final: 0.8363 (t0) REVERT: A 882 ASP cc_start: 0.7819 (p0) cc_final: 0.7407 (p0) REVERT: A 1035 MET cc_start: 0.7219 (tmm) cc_final: 0.6527 (tmm) REVERT: B 437 ILE cc_start: 0.6492 (mt) cc_final: 0.6149 (mt) REVERT: C 236 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6674 (mt-10) REVERT: C 278 CYS cc_start: 0.7045 (t) cc_final: 0.6738 (m) REVERT: C 337 SER cc_start: 0.7876 (t) cc_final: 0.7633 (p) REVERT: C 421 MET cc_start: 0.7256 (tmm) cc_final: 0.6932 (ppp) outliers start: 25 outliers final: 16 residues processed: 215 average time/residue: 0.1109 time to fit residues: 35.5272 Evaluate side-chains 204 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 371 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 86 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 93 optimal weight: 0.4980 chunk 44 optimal weight: 0.0470 chunk 92 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 59 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN A 928 ASN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.127916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.104176 restraints weight = 29306.393| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.77 r_work: 0.3594 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14425 Z= 0.106 Angle : 0.523 8.290 19725 Z= 0.267 Chirality : 0.038 0.165 2115 Planarity : 0.004 0.037 2389 Dihedral : 14.515 59.923 2241 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.83 % Allowed : 11.96 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.68 (0.22), residues: 1604 helix: 1.33 (0.21), residues: 663 sheet: -0.68 (0.34), residues: 233 loop : 0.16 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 325 TYR 0.017 0.001 TYR C 478 PHE 0.018 0.001 PHE A 591 TRP 0.029 0.001 TRP A 896 HIS 0.003 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00229 (14425) covalent geometry : angle 0.52281 (19725) hydrogen bonds : bond 0.03394 ( 635) hydrogen bonds : angle 4.87941 ( 1750) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 ARG cc_start: 0.8423 (tpp-160) cc_final: 0.8215 (tpp-160) REVERT: A 381 ASP cc_start: 0.8594 (m-30) cc_final: 0.8336 (t0) REVERT: A 1035 MET cc_start: 0.6932 (tmm) cc_final: 0.6348 (tmm) REVERT: B 253 ASP cc_start: 0.8213 (t70) cc_final: 0.7934 (t0) REVERT: B 437 ILE cc_start: 0.6123 (mt) cc_final: 0.5852 (mt) REVERT: B 449 GLU cc_start: 0.7595 (mp0) cc_final: 0.7278 (mp0) REVERT: C 278 CYS cc_start: 0.7225 (t) cc_final: 0.6804 (m) REVERT: C 421 MET cc_start: 0.7181 (tmm) cc_final: 0.6804 (ppp) REVERT: C 465 MET cc_start: 0.8048 (mmt) cc_final: 0.7755 (mmt) outliers start: 26 outliers final: 12 residues processed: 228 average time/residue: 0.1201 time to fit residues: 40.7296 Evaluate side-chains 200 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 148 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 758 GLN B 216 HIS ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.124730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.100722 restraints weight = 29380.469| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.79 r_work: 0.3541 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14425 Z= 0.199 Angle : 0.577 9.030 19725 Z= 0.294 Chirality : 0.041 0.171 2115 Planarity : 0.004 0.043 2389 Dihedral : 14.584 60.894 2239 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.53 % Allowed : 12.74 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.52 (0.22), residues: 1604 helix: 1.22 (0.20), residues: 649 sheet: -0.75 (0.34), residues: 233 loop : 0.06 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 203 TYR 0.016 0.002 TYR C 291 PHE 0.022 0.002 PHE C 254 TRP 0.027 0.002 TRP A 896 HIS 0.007 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00461 (14425) covalent geometry : angle 0.57729 (19725) hydrogen bonds : bond 0.03783 ( 635) hydrogen bonds : angle 4.97026 ( 1750) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 ASP cc_start: 0.8615 (m-30) cc_final: 0.8388 (t0) REVERT: A 896 TRP cc_start: 0.8100 (t60) cc_final: 0.7797 (t-100) REVERT: A 922 GLU cc_start: 0.7801 (tp30) cc_final: 0.7312 (tp30) REVERT: B 215 PHE cc_start: 0.7312 (m-10) cc_final: 0.7066 (m-10) REVERT: B 437 ILE cc_start: 0.6327 (mt) cc_final: 0.5944 (mt) REVERT: B 449 GLU cc_start: 0.7593 (mp0) cc_final: 0.7218 (mp0) REVERT: B 450 ASN cc_start: 0.8705 (p0) cc_final: 0.8496 (p0) REVERT: C 278 CYS cc_start: 0.7151 (t) cc_final: 0.6783 (m) REVERT: C 291 TYR cc_start: 0.7874 (t80) cc_final: 0.7641 (t80) REVERT: C 421 MET cc_start: 0.7306 (tmm) cc_final: 0.6906 (ppp) REVERT: C 465 MET cc_start: 0.7987 (mmt) cc_final: 0.7712 (mmt) outliers start: 36 outliers final: 23 residues processed: 216 average time/residue: 0.1083 time to fit residues: 34.6705 Evaluate side-chains 204 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 124 GLN Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 5 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 GLN B 216 HIS C 84 GLN ** C 323 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 = 0.4076 r_free = 0.4076 target = 0.124242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.100267 restraints weight = 29448.225| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.80 r_work: 0.3533 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14425 Z= 0.201 Angle : 0.586 9.031 19725 Z= 0.298 Chirality : 0.041 0.170 2115 Planarity : 0.004 0.045 2389 Dihedral : 14.649 61.597 2239 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.81 % Allowed : 13.72 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.37 (0.22), residues: 1604 helix: 1.09 (0.20), residues: 656 sheet: -0.85 (0.34), residues: 233 loop : -0.02 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 203 TYR 0.015 0.002 TYR C 291 PHE 0.021 0.002 PHE C 254 TRP 0.014 0.001 TRP A 875 HIS 0.006 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00468 (14425) covalent geometry : angle 0.58617 (19725) hydrogen bonds : bond 0.03762 ( 635) hydrogen bonds : angle 4.96190 ( 1750) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.8029 (tp30) cc_final: 0.7805 (tt0) REVERT: A 381 ASP cc_start: 0.8635 (m-30) cc_final: 0.8390 (t0) REVERT: A 896 TRP cc_start: 0.8155 (t60) cc_final: 0.7921 (t-100) REVERT: A 922 GLU cc_start: 0.7711 (tp30) cc_final: 0.7224 (tp30) REVERT: A 943 LEU cc_start: 0.8120 (mt) cc_final: 0.7786 (mt) REVERT: B 449 GLU cc_start: 0.7602 (mp0) cc_final: 0.7259 (mp0) REVERT: C 278 CYS cc_start: 0.7160 (t) cc_final: 0.6788 (m) REVERT: C 421 MET cc_start: 0.7354 (tmm) cc_final: 0.6988 (ppp) REVERT: C 465 MET cc_start: 0.7860 (mmt) cc_final: 0.7574 (mmt) outliers start: 40 outliers final: 22 residues processed: 220 average time/residue: 0.1198 time to fit residues: 39.0336 Evaluate side-chains 201 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 73 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 147 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN B 216 HIS ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.126209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.102197 restraints weight = 29208.376| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.86 r_work: 0.3556 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14425 Z= 0.131 Angle : 0.541 9.619 19725 Z= 0.275 Chirality : 0.039 0.164 2115 Planarity : 0.004 0.043 2389 Dihedral : 14.439 60.850 2236 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.97 % Allowed : 14.43 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.53 (0.22), residues: 1604 helix: 1.23 (0.20), residues: 664 sheet: -0.74 (0.34), residues: 225 loop : 0.04 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 203 TYR 0.019 0.001 TYR C 291 PHE 0.014 0.001 PHE B 403 TRP 0.016 0.001 TRP B 241 HIS 0.004 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00302 (14425) covalent geometry : angle 0.54067 (19725) hydrogen bonds : bond 0.03368 ( 635) hydrogen bonds : angle 4.70200 ( 1750) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.8048 (tp30) cc_final: 0.7814 (tt0) REVERT: A 381 ASP cc_start: 0.8618 (m-30) cc_final: 0.8375 (t0) REVERT: A 922 GLU cc_start: 0.7718 (tp30) cc_final: 0.7207 (tp30) REVERT: A 943 LEU cc_start: 0.8044 (mt) cc_final: 0.7686 (mt) REVERT: A 945 MET cc_start: 0.6826 (tpp) cc_final: 0.6575 (mmt) REVERT: B 449 GLU cc_start: 0.7699 (mp0) cc_final: 0.7287 (mp0) REVERT: B 450 ASN cc_start: 0.8694 (p0) cc_final: 0.8469 (p0) REVERT: C 197 LEU cc_start: 0.4738 (OUTLIER) cc_final: 0.4432 (mt) REVERT: C 278 CYS cc_start: 0.7261 (t) cc_final: 0.6815 (m) REVERT: C 291 TYR cc_start: 0.7891 (t80) cc_final: 0.7560 (t80) REVERT: C 421 MET cc_start: 0.7399 (tmm) cc_final: 0.7072 (ppp) REVERT: C 465 MET cc_start: 0.7895 (mmt) cc_final: 0.7591 (mmt) outliers start: 28 outliers final: 20 residues processed: 218 average time/residue: 0.1221 time to fit residues: 39.3100 Evaluate side-chains 202 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 89 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.124783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.100778 restraints weight = 29143.569| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.84 r_work: 0.3535 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14425 Z= 0.198 Angle : 0.594 9.352 19725 Z= 0.302 Chirality : 0.041 0.162 2115 Planarity : 0.004 0.044 2389 Dihedral : 14.491 61.628 2236 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.18 % Allowed : 15.13 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.34 (0.21), residues: 1604 helix: 1.06 (0.20), residues: 656 sheet: -0.80 (0.34), residues: 225 loop : -0.07 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 203 TYR 0.016 0.002 TYR C 291 PHE 0.021 0.002 PHE C 254 TRP 0.013 0.001 TRP C 304 HIS 0.007 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00463 (14425) covalent geometry : angle 0.59423 (19725) hydrogen bonds : bond 0.03690 ( 635) hydrogen bonds : angle 4.85584 ( 1750) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.8009 (tp30) cc_final: 0.7783 (tt0) REVERT: A 381 ASP cc_start: 0.8628 (m-30) cc_final: 0.8396 (t0) REVERT: A 922 GLU cc_start: 0.7742 (tp30) cc_final: 0.7229 (tp30) REVERT: A 943 LEU cc_start: 0.8131 (mt) cc_final: 0.7786 (mt) REVERT: B 253 ASP cc_start: 0.8356 (t70) cc_final: 0.8065 (t0) REVERT: B 449 GLU cc_start: 0.7659 (mp0) cc_final: 0.7246 (mp0) REVERT: B 450 ASN cc_start: 0.8716 (p0) cc_final: 0.8483 (p0) REVERT: C 252 LEU cc_start: 0.8139 (tp) cc_final: 0.7919 (tt) REVERT: C 278 CYS cc_start: 0.7168 (t) cc_final: 0.6757 (m) REVERT: C 421 MET cc_start: 0.7426 (tmm) cc_final: 0.7081 (ppp) REVERT: C 465 MET cc_start: 0.7837 (mmt) cc_final: 0.7550 (mmt) outliers start: 31 outliers final: 28 residues processed: 209 average time/residue: 0.1228 time to fit residues: 37.8838 Evaluate side-chains 208 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 1 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 HIS ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.126472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.102450 restraints weight = 29094.430| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.86 r_work: 0.3569 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14425 Z= 0.126 Angle : 0.551 10.298 19725 Z= 0.278 Chirality : 0.039 0.163 2115 Planarity : 0.004 0.043 2389 Dihedral : 14.348 61.349 2236 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.76 % Allowed : 15.69 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.56 (0.22), residues: 1604 helix: 1.24 (0.20), residues: 666 sheet: -0.62 (0.35), residues: 225 loop : 0.01 (0.25), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 203 TYR 0.016 0.001 TYR C 291 PHE 0.014 0.001 PHE B 403 TRP 0.023 0.001 TRP C 304 HIS 0.004 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00291 (14425) covalent geometry : angle 0.55061 (19725) hydrogen bonds : bond 0.03305 ( 635) hydrogen bonds : angle 4.63067 ( 1750) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.8023 (tp30) cc_final: 0.7810 (tt0) REVERT: A 381 ASP cc_start: 0.8602 (m-30) cc_final: 0.8362 (t0) REVERT: A 855 MET cc_start: 0.8913 (mmm) cc_final: 0.8411 (mmm) REVERT: A 922 GLU cc_start: 0.7700 (tp30) cc_final: 0.7170 (tp30) REVERT: B 301 GLU cc_start: 0.7955 (tt0) cc_final: 0.7711 (mt-10) REVERT: B 449 GLU cc_start: 0.7635 (mp0) cc_final: 0.7210 (mp0) REVERT: B 450 ASN cc_start: 0.8704 (p0) cc_final: 0.8491 (p0) REVERT: C 278 CYS cc_start: 0.7273 (t) cc_final: 0.6850 (m) REVERT: C 291 TYR cc_start: 0.7782 (t80) cc_final: 0.7533 (t80) REVERT: C 421 MET cc_start: 0.7529 (tmm) cc_final: 0.7219 (ppp) REVERT: C 465 MET cc_start: 0.7823 (mmt) cc_final: 0.7527 (mmt) outliers start: 25 outliers final: 21 residues processed: 210 average time/residue: 0.1185 time to fit residues: 36.9538 Evaluate side-chains 204 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 109 optimal weight: 0.1980 chunk 4 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN B 216 HIS ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.125183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.101426 restraints weight = 29256.901| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.80 r_work: 0.3551 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14425 Z= 0.175 Angle : 0.587 10.327 19725 Z= 0.296 Chirality : 0.040 0.163 2115 Planarity : 0.004 0.043 2389 Dihedral : 14.376 62.081 2236 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.04 % Allowed : 15.76 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.43 (0.21), residues: 1604 helix: 1.12 (0.20), residues: 662 sheet: -0.71 (0.35), residues: 225 loop : -0.04 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 203 TYR 0.016 0.002 TYR C 291 PHE 0.020 0.002 PHE C 254 TRP 0.025 0.001 TRP C 304 HIS 0.006 0.001 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00410 (14425) covalent geometry : angle 0.58749 (19725) hydrogen bonds : bond 0.03575 ( 635) hydrogen bonds : angle 4.72656 ( 1750) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 ASP cc_start: 0.8594 (m-30) cc_final: 0.8367 (t0) REVERT: A 922 GLU cc_start: 0.7723 (tp30) cc_final: 0.7211 (tp30) REVERT: B 253 ASP cc_start: 0.8317 (t70) cc_final: 0.8039 (t0) REVERT: B 449 GLU cc_start: 0.7645 (mp0) cc_final: 0.7235 (mp0) REVERT: B 450 ASN cc_start: 0.8746 (p0) cc_final: 0.8520 (p0) REVERT: C 278 CYS cc_start: 0.7226 (t) cc_final: 0.6848 (m) REVERT: C 291 TYR cc_start: 0.7763 (t80) cc_final: 0.7291 (t80) REVERT: C 421 MET cc_start: 0.7570 (tmm) cc_final: 0.7269 (ppp) REVERT: C 465 MET cc_start: 0.7790 (mmt) cc_final: 0.7515 (mmt) outliers start: 29 outliers final: 25 residues processed: 211 average time/residue: 0.1198 time to fit residues: 37.5114 Evaluate side-chains 203 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 313 HIS Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.0370 chunk 71 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN A 954 GLN B 216 HIS ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.123484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.098942 restraints weight = 29306.706| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.04 r_work: 0.3470 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14425 Z= 0.146 Angle : 0.581 10.485 19725 Z= 0.293 Chirality : 0.040 0.177 2115 Planarity : 0.004 0.043 2389 Dihedral : 14.316 62.167 2236 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.97 % Allowed : 15.97 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.52 (0.21), residues: 1604 helix: 1.21 (0.20), residues: 666 sheet: -0.70 (0.35), residues: 225 loop : 0.01 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 931 TYR 0.015 0.001 TYR B 291 PHE 0.020 0.002 PHE A 939 TRP 0.037 0.001 TRP C 304 HIS 0.006 0.001 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00341 (14425) covalent geometry : angle 0.58138 (19725) hydrogen bonds : bond 0.03422 ( 635) hydrogen bonds : angle 4.62773 ( 1750) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 ASP cc_start: 0.8636 (m-30) cc_final: 0.8393 (t0) REVERT: A 855 MET cc_start: 0.9023 (mmm) cc_final: 0.8521 (mmm) REVERT: A 896 TRP cc_start: 0.8051 (t-100) cc_final: 0.7706 (t-100) REVERT: A 922 GLU cc_start: 0.7708 (tp30) cc_final: 0.7198 (tp30) REVERT: B 449 GLU cc_start: 0.7686 (mp0) cc_final: 0.7252 (mp0) REVERT: B 450 ASN cc_start: 0.8757 (p0) cc_final: 0.8556 (p0) REVERT: C 278 CYS cc_start: 0.7393 (t) cc_final: 0.6939 (m) REVERT: C 301 GLU cc_start: 0.7421 (tt0) cc_final: 0.7199 (tt0) REVERT: C 421 MET cc_start: 0.7631 (tmm) cc_final: 0.7321 (ppp) REVERT: C 465 MET cc_start: 0.7881 (mmt) cc_final: 0.7596 (mmt) outliers start: 28 outliers final: 26 residues processed: 210 average time/residue: 0.1226 time to fit residues: 37.8644 Evaluate side-chains 209 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 90 optimal weight: 0.0370 chunk 76 optimal weight: 0.9990 chunk 83 optimal weight: 0.0470 chunk 114 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 chunk 110 optimal weight: 0.0000 chunk 17 optimal weight: 0.0060 chunk 96 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.1776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 ASN A 946 GLN B 216 HIS B 409 ASN C 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.126416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.101825 restraints weight = 29366.703| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.09 r_work: 0.3521 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14425 Z= 0.108 Angle : 0.568 10.656 19725 Z= 0.287 Chirality : 0.039 0.177 2115 Planarity : 0.004 0.042 2389 Dihedral : 14.161 61.266 2236 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.48 % Allowed : 16.54 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.71 (0.22), residues: 1604 helix: 1.42 (0.21), residues: 666 sheet: -0.61 (0.35), residues: 227 loop : 0.06 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 203 TYR 0.018 0.001 TYR C 291 PHE 0.032 0.001 PHE A 939 TRP 0.047 0.001 TRP C 304 HIS 0.007 0.001 HIS C 323 Details of bonding type rmsd covalent geometry : bond 0.00237 (14425) covalent geometry : angle 0.56781 (19725) hydrogen bonds : bond 0.03185 ( 635) hydrogen bonds : angle 4.44242 ( 1750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3186.18 seconds wall clock time: 55 minutes 28.66 seconds (3328.66 seconds total)