Starting phenix.real_space_refine on Fri Jul 3 11:44:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ic0_52823/07_2026/9ic0_52823.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ic0_52823/07_2026/9ic0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ic0_52823/07_2026/9ic0_52823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ic0_52823/07_2026/9ic0_52823.map" model { file = "/net/cci-nas-00/data/ceres_data/9ic0_52823/07_2026/9ic0_52823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ic0_52823/07_2026/9ic0_52823.cif" } 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-dev-6108/lib/python3.11/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, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'DCP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 3.39, 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: 1.12 Conformation dependent library (CDL) restraints added in 654.2 milliseconds 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: 1.64 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: 2.79 Time building geometry restraints manager: 1.52 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 1.420 1.619 -0.199 2.00e-02 2.50e+03 9.85e+01 bond pdb=" C3' DCP A1301 " pdb=" C4' DCP A1301 " ideal model delta sigma weight residual 1.534 1.343 0.191 2.00e-02 2.50e+03 9.07e+01 bond pdb=" C5 DCP A1301 " pdb=" C6 DCP A1301 " ideal model delta sigma weight residual 1.347 1.501 -0.154 2.00e-02 2.50e+03 5.97e+01 bond pdb=" C2 DCP A1301 " pdb=" N3 DCP A1301 " ideal model delta sigma weight residual 1.350 1.504 -0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" C4 DCP A1301 " pdb=" N3 DCP A1301 " ideal model delta sigma weight residual 1.317 1.455 -0.138 2.00e-02 2.50e+03 4.75e+01 ... (remaining 14420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 19522 2.41 - 4.82: 179 4.82 - 7.22: 18 7.22 - 9.63: 4 9.63 - 12.04: 2 Bond angle restraints: 19725 Sorted by residual: angle pdb=" N3 DT T 24 " pdb=" C4 DT T 24 " pdb=" O4 DT T 24 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+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 angle pdb=" N3 DT T 22 " pdb=" C4 DT T 22 " pdb=" O4 DT T 22 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT T 29 " pdb=" C4 DT T 29 " pdb=" O4 DT T 29 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT P 9 " pdb=" C4 DT P 9 " pdb=" O4 DT P 9 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 19720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 7684 15.99 - 31.98: 542 31.98 - 47.97: 169 47.97 - 63.96: 85 63.96 - 79.94: 4 Dihedral angle restraints: 8484 sinusoidal: 3774 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 8481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1399 0.033 - 0.066: 508 0.066 - 0.099: 142 0.099 - 0.132: 62 0.132 - 0.165: 4 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 -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.82e-01 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=" C1' DCP A1301 " pdb=" C2' DCP A1301 " pdb=" N1 DCP A1301 " pdb=" O4' DCP A1301 " both_signs ideal model delta sigma weight residual False 2.25 2.39 -0.14 2.00e-01 2.50e+01 4.72e-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 3.250 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 3.250 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: 3.070 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.300 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 0.199 14425 Z= 0.299 Angle : 0.588 12.039 19725 Z= 0.363 Chirality : 0.039 0.165 2115 Planarity : 0.004 0.032 2389 Dihedral : 13.427 79.945 5444 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 are 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/Z covalent geometry : bond 0.00494 / 0.30 (14425) covalent geometry : angle 0.58759 / 0.36 (19725) hydrogen bonds : bond 0.18340 / 12.44 ( 635) hydrogen bonds : angle 6.98403 / 5.08 ( 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 : 0.550 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: 0.1225 time to fit residues: 47.9163 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 : 0.526 ------------------------------------------------------------------------------- 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: 0.9980 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: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4078 r_free = 0.4078 target = 0.124451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.100395 restraints weight = 29392.556| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.85 r_work: 0.3529 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1281 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= 0.227 Angle : 0.640 7.912 19725 Z= 0.330 Chirality : 0.043 0.165 2115 Planarity : 0.005 0.039 2389 Dihedral : 14.709 59.983 2251 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.69 % Allowed : 10.70 % Favored : 87.61 % 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 are not related in a simple way. whole: 0.32 (0.21), residues: 1604 helix: 1.02 (0.20), residues: 645 sheet: -0.80 (0.33), residues: 245 loop : -0.01 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 805 TYR 0.015 0.002 TYR C 193 PHE 0.020 0.002 PHE A 180 TRP 0.013 0.002 TRP B 241 HIS 0.007 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.23 (14425) covalent geometry : angle 0.64041 / 0.33 (19725) hydrogen bonds : bond 0.04848 / 3.29 ( 635) hydrogen bonds : angle 5.63080 / 4.13 ( 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: 24 poor density : 201 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 ASP cc_start: 0.8609 (m-30) cc_final: 0.8373 (t0) REVERT: A 882 ASP cc_start: 0.7801 (p0) cc_final: 0.7408 (p0) REVERT: A 1032 GLU cc_start: 0.4326 (pm20) cc_final: 0.4078 (pm20) REVERT: A 1035 MET cc_start: 0.7137 (tmm) cc_final: 0.6445 (tmm) REVERT: B 437 ILE cc_start: 0.6315 (mt) cc_final: 0.5999 (mt) REVERT: C 278 CYS cc_start: 0.6948 (t) cc_final: 0.6646 (m) REVERT: C 323 HIS cc_start: 0.5093 (m-70) cc_final: 0.4841 (m-70) REVERT: C 337 SER cc_start: 0.7808 (t) cc_final: 0.7581 (p) REVERT: C 421 MET cc_start: 0.6901 (tmm) cc_final: 0.6555 (ppp) REVERT: C 465 MET cc_start: 0.8145 (mmt) cc_final: 0.7829 (mmt) outliers start: 24 outliers final: 13 residues processed: 216 average time/residue: 0.1142 time to fit residues: 37.0452 Evaluate side-chains 202 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 747 ASP 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 C residue 95 CYS 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 86 optimal weight: 0.8980 chunk 145 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 164 optimal weight: 40.0000 chunk 149 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 ASN A 928 ASN B 323 HIS C 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.126117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.102194 restraints weight = 29400.064| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.81 r_work: 0.3564 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14425 Z= 0.138 Angle : 0.557 8.781 19725 Z= 0.289 Chirality : 0.040 0.173 2115 Planarity : 0.004 0.040 2389 Dihedral : 14.689 61.089 2246 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.32 % Allowed : 11.33 % Favored : 86.35 % 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 are not related in a simple way. whole: 0.46 (0.22), residues: 1604 helix: 1.17 (0.21), residues: 652 sheet: -0.83 (0.34), residues: 243 loop : 0.06 (0.25), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 638 TYR 0.017 0.001 TYR C 478 PHE 0.026 0.002 PHE A 591 TRP 0.031 0.001 TRP A 896 HIS 0.004 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (14425) covalent geometry : angle 0.55712 / 0.29 (19725) hydrogen bonds : bond 0.03991 / 2.72 ( 635) hydrogen bonds : angle 5.19977 / 3.83 ( 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 232 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 ASP cc_start: 0.8626 (m-30) cc_final: 0.8380 (t0) REVERT: A 728 PHE cc_start: 0.7126 (m-80) cc_final: 0.6776 (m-80) REVERT: A 1035 MET cc_start: 0.7050 (tmm) cc_final: 0.6377 (tmm) REVERT: B 306 LEU cc_start: 0.8464 (mp) cc_final: 0.8244 (mm) REVERT: B 437 ILE cc_start: 0.6211 (mt) cc_final: 0.5892 (mt) REVERT: B 449 GLU cc_start: 0.7543 (mp0) cc_final: 0.7273 (mp0) REVERT: C 278 CYS cc_start: 0.6928 (t) cc_final: 0.6634 (m) REVERT: C 337 SER cc_start: 0.7874 (t) cc_final: 0.7657 (p) REVERT: C 421 MET cc_start: 0.7030 (tmm) cc_final: 0.6583 (ppp) REVERT: C 465 MET cc_start: 0.8161 (mmt) cc_final: 0.7843 (mmt) outliers start: 33 outliers final: 15 residues processed: 219 average time/residue: 0.1126 time to fit residues: 36.8832 Evaluate side-chains 204 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 365 ARG Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 1131 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 303 LEU Chi-restraints excluded: chain B residue 323 HIS 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 206 TYR Chi-restraints excluded: chain C residue 332 VAL 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: 5.9990 chunk 133 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 164 optimal weight: 30.0000 chunk 36 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 GLN B 216 HIS B 323 HIS C 84 GLN C 132 HIS ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.124030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.100120 restraints weight = 29404.729| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.77 r_work: 0.3534 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14425 Z= 0.237 Angle : 0.627 8.998 19725 Z= 0.320 Chirality : 0.042 0.164 2115 Planarity : 0.005 0.045 2389 Dihedral : 14.825 61.681 2242 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.46 % Allowed : 12.17 % Favored : 85.36 % 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 are not related in a simple way. whole: 0.28 (0.22), residues: 1604 helix: 1.04 (0.21), residues: 646 sheet: -0.85 (0.33), residues: 245 loop : -0.08 (0.25), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 325 TYR 0.016 0.002 TYR C 291 PHE 0.022 0.002 PHE C 254 TRP 0.030 0.002 TRP A 896 HIS 0.009 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 (14425) covalent geometry : angle 0.62670 / 0.32 (19725) hydrogen bonds : bond 0.04180 / 2.83 ( 635) hydrogen bonds : angle 5.24854 / 3.86 ( 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 228 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 ASP cc_start: 0.8672 (m-30) cc_final: 0.8410 (t0) REVERT: A 728 PHE cc_start: 0.7193 (m-80) cc_final: 0.6917 (m-80) REVERT: A 922 GLU cc_start: 0.7735 (tp30) cc_final: 0.7251 (tp30) REVERT: A 1035 MET cc_start: 0.7159 (tmm) cc_final: 0.6491 (tmm) REVERT: A 1141 MET cc_start: 0.7984 (tpt) cc_final: 0.7681 (tpp) REVERT: B 253 ASP cc_start: 0.8341 (t70) cc_final: 0.8041 (t0) REVERT: B 386 ASP cc_start: 0.7967 (t0) cc_final: 0.7602 (t0) REVERT: B 437 ILE cc_start: 0.6394 (mt) cc_final: 0.6020 (mt) REVERT: B 445 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7941 (mt-10) REVERT: B 449 GLU cc_start: 0.7619 (mp0) cc_final: 0.7307 (mp0) REVERT: C 236 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6644 (mt-10) REVERT: C 278 CYS cc_start: 0.7162 (t) cc_final: 0.6787 (m) REVERT: C 421 MET cc_start: 0.7160 (tmm) cc_final: 0.6641 (ppp) REVERT: C 465 MET cc_start: 0.7963 (mmt) cc_final: 0.7663 (mmt) outliers start: 35 outliers final: 24 residues processed: 217 average time/residue: 0.1050 time to fit residues: 34.4854 Evaluate side-chains 208 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU 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 1112 HIS 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 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 323 HIS Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 418 LEU 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 206 TYR Chi-restraints excluded: chain C residue 300 ILE 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: 0.0670 chunk 72 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 ASN B 216 HIS B 323 HIS C 84 GLN ** C 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.126559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.102586 restraints weight = 29270.125| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.80 r_work: 0.3570 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1841 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= 0.128 Angle : 0.546 9.577 19725 Z= 0.282 Chirality : 0.039 0.165 2115 Planarity : 0.004 0.042 2389 Dihedral : 14.768 61.503 2242 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.32 % Allowed : 13.37 % Favored : 84.31 % 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 are not related in a simple way. whole: 0.42 (0.22), residues: 1604 helix: 1.11 (0.20), residues: 655 sheet: -0.82 (0.34), residues: 235 loop : 0.03 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 344 TYR 0.016 0.001 TYR C 291 PHE 0.024 0.001 PHE A 591 TRP 0.040 0.001 TRP A 896 HIS 0.011 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (14425) covalent geometry : angle 0.54632 / 0.28 (19725) hydrogen bonds : bond 0.03666 / 2.49 ( 635) hydrogen bonds : angle 5.01424 / 3.69 ( 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 227 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 381 ASP cc_start: 0.8631 (m-30) cc_final: 0.8390 (t0) REVERT: A 728 PHE cc_start: 0.7108 (m-80) cc_final: 0.6894 (m-80) REVERT: A 922 GLU cc_start: 0.7728 (tp30) cc_final: 0.7234 (tp30) REVERT: A 943 LEU cc_start: 0.8133 (mt) cc_final: 0.7706 (mt) REVERT: A 1035 MET cc_start: 0.7085 (tmm) cc_final: 0.6502 (tmm) REVERT: A 1141 MET cc_start: 0.7935 (tpt) cc_final: 0.7575 (tpp) REVERT: B 338 VAL cc_start: 0.9382 (OUTLIER) cc_final: 0.9128 (t) REVERT: B 437 ILE cc_start: 0.6148 (mt) cc_final: 0.5791 (mt) REVERT: B 449 GLU cc_start: 0.7620 (mp0) cc_final: 0.7288 (mp0) REVERT: C 236 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6554 (mt-10) REVERT: C 278 CYS cc_start: 0.7011 (t) cc_final: 0.6697 (m) REVERT: C 313 HIS cc_start: 0.7440 (OUTLIER) cc_final: 0.7172 (p-80) REVERT: C 421 MET cc_start: 0.7105 (tmm) cc_final: 0.6642 (ppp) REVERT: C 465 MET cc_start: 0.7970 (mmt) cc_final: 0.7650 (mmt) outliers start: 33 outliers final: 18 residues processed: 214 average time/residue: 0.1119 time to fit residues: 35.7542 Evaluate side-chains 203 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 827 THR 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 187 HIS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 104 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 73 optimal weight: 5.9990 chunk 16 optimal weight: 0.0070 chunk 123 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 758 GLN B 216 HIS ** B 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4096 r_free = 0.4096 target = 0.125315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.101269 restraints weight = 29253.111| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.80 r_work: 0.3555 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1972 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= 0.171 Angle : 0.577 9.939 19725 Z= 0.295 Chirality : 0.041 0.162 2115 Planarity : 0.004 0.043 2389 Dihedral : 14.778 61.566 2242 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.18 % Allowed : 14.29 % Favored : 83.53 % 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 are not related in a simple way. whole: 0.42 (0.21), residues: 1604 helix: 1.10 (0.20), residues: 649 sheet: -0.82 (0.33), residues: 231 loop : 0.04 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 203 TYR 0.021 0.002 TYR C 291 PHE 0.020 0.002 PHE A 591 TRP 0.065 0.001 TRP A 896 HIS 0.011 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (14425) covalent geometry : angle 0.57685 / 0.30 (19725) hydrogen bonds : bond 0.03767 / 2.55 ( 635) hydrogen bonds : angle 5.00325 / 3.65 ( 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 224 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ILE cc_start: 0.8836 (mp) cc_final: 0.8598 (mp) REVERT: A 381 ASP cc_start: 0.8616 (m-30) cc_final: 0.8393 (t0) REVERT: A 922 GLU cc_start: 0.7767 (tp30) cc_final: 0.7254 (tp30) REVERT: A 1141 MET cc_start: 0.8021 (tpt) cc_final: 0.7661 (tpp) REVERT: B 215 PHE cc_start: 0.7232 (m-10) cc_final: 0.7003 (m-10) REVERT: B 386 ASP cc_start: 0.7908 (t0) cc_final: 0.7555 (t0) REVERT: B 449 GLU cc_start: 0.7673 (mp0) cc_final: 0.7351 (mp0) REVERT: C 236 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6644 (mt-10) REVERT: C 278 CYS cc_start: 0.7041 (t) cc_final: 0.6689 (m) REVERT: C 291 TYR cc_start: 0.7851 (t80) cc_final: 0.7614 (t80) REVERT: C 313 HIS cc_start: 0.7453 (OUTLIER) cc_final: 0.7247 (p-80) REVERT: C 421 MET cc_start: 0.7256 (tmm) cc_final: 0.6829 (ppp) REVERT: C 465 MET cc_start: 0.7995 (mmt) cc_final: 0.7682 (mmt) outliers start: 31 outliers final: 20 residues processed: 213 average time/residue: 0.1177 time to fit residues: 37.0404 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 : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 230 LEU 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 1131 LEU 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 303 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 383 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 89 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 9.9990 chunk 162 optimal weight: 30.0000 chunk 119 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 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 = 0.4096 r_free = 0.4096 target = 0.125399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.101390 restraints weight = 29092.037| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.78 r_work: 0.3561 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 : 0.004 0.077 14425 Z= 0.173 Angle : 0.596 10.436 19725 Z= 0.304 Chirality : 0.041 0.252 2115 Planarity : 0.004 0.049 2389 Dihedral : 14.787 61.685 2242 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.11 % Allowed : 14.64 % Favored : 83.25 % 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 are not related in a simple way. whole: 0.38 (0.21), residues: 1604 helix: 1.08 (0.20), residues: 647 sheet: -0.80 (0.33), residues: 231 loop : -0.01 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 203 TYR 0.018 0.002 TYR C 291 PHE 0.026 0.002 PHE A 591 TRP 0.079 0.002 TRP A 896 HIS 0.011 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (14425) covalent geometry : angle 0.59581 / 0.30 (19725) hydrogen bonds : bond 0.03755 / 2.56 ( 635) hydrogen bonds : angle 4.99861 / 3.63 ( 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 222 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ILE cc_start: 0.8839 (mp) cc_final: 0.8593 (mp) REVERT: A 214 GLU cc_start: 0.8065 (tp30) cc_final: 0.7808 (tt0) REVERT: A 381 ASP cc_start: 0.8638 (m-30) cc_final: 0.8398 (t0) REVERT: A 922 GLU cc_start: 0.7750 (tp30) cc_final: 0.7235 (tp30) REVERT: A 1141 MET cc_start: 0.7995 (tpt) cc_final: 0.7622 (tpp) REVERT: B 386 ASP cc_start: 0.7951 (t0) cc_final: 0.7611 (t0) REVERT: B 449 GLU cc_start: 0.7695 (mp0) cc_final: 0.7353 (mp0) REVERT: C 236 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6635 (mt-10) REVERT: C 278 CYS cc_start: 0.7301 (t) cc_final: 0.6847 (m) REVERT: C 291 TYR cc_start: 0.7925 (t80) cc_final: 0.7618 (t80) REVERT: C 313 HIS cc_start: 0.7489 (OUTLIER) cc_final: 0.7272 (p-80) REVERT: C 421 MET cc_start: 0.7279 (tmm) cc_final: 0.6827 (ppp) REVERT: C 465 MET cc_start: 0.7907 (mmt) cc_final: 0.7587 (mmt) outliers start: 30 outliers final: 23 residues processed: 211 average time/residue: 0.1150 time to fit residues: 36.2038 Evaluate side-chains 212 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU 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 909 LEU Chi-restraints excluded: chain A residue 943 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 79 LEU 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 337 SER Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 104 VAL 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: 0.8980 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 GLN B 216 HIS B 323 HIS ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4112 r_free = 0.4112 target = 0.126390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.102216 restraints weight = 29188.933| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.87 r_work: 0.3565 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14425 Z= 0.135 Angle : 0.571 10.640 19725 Z= 0.293 Chirality : 0.040 0.233 2115 Planarity : 0.004 0.043 2389 Dihedral : 14.741 61.504 2242 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.18 % Allowed : 14.99 % Favored : 82.83 % 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 are not related in a simple way. whole: 0.45 (0.21), residues: 1604 helix: 1.17 (0.21), residues: 653 sheet: -0.67 (0.34), residues: 225 loop : -0.05 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 203 TYR 0.017 0.001 TYR C 291 PHE 0.019 0.001 PHE A 591 TRP 0.079 0.001 TRP A 896 HIS 0.011 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14425) covalent geometry : angle 0.57076 / 0.29 (19725) hydrogen bonds : bond 0.03525 / 2.40 ( 635) hydrogen bonds : angle 4.87443 / 3.53 ( 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 225 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ILE cc_start: 0.8773 (mp) cc_final: 0.8517 (mp) REVERT: A 214 GLU cc_start: 0.8025 (tp30) cc_final: 0.7787 (tt0) REVERT: A 381 ASP cc_start: 0.8623 (m-30) cc_final: 0.8386 (t0) REVERT: A 922 GLU cc_start: 0.7771 (tp30) cc_final: 0.7265 (tp30) REVERT: A 1141 MET cc_start: 0.8003 (tpt) cc_final: 0.7603 (tpp) REVERT: B 253 ASP cc_start: 0.8265 (t70) cc_final: 0.7975 (t0) REVERT: B 301 GLU cc_start: 0.7991 (tp30) cc_final: 0.7669 (mm-30) REVERT: B 386 ASP cc_start: 0.7931 (t0) cc_final: 0.7603 (t0) REVERT: B 449 GLU cc_start: 0.7696 (mp0) cc_final: 0.7361 (mp0) REVERT: C 236 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6648 (mt-10) REVERT: C 278 CYS cc_start: 0.7170 (t) cc_final: 0.6739 (m) REVERT: C 291 TYR cc_start: 0.7915 (t80) cc_final: 0.7626 (t80) REVERT: C 301 GLU cc_start: 0.7295 (tt0) cc_final: 0.7076 (tt0) REVERT: C 313 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.7235 (p-80) REVERT: C 421 MET cc_start: 0.7294 (tmm) cc_final: 0.6874 (ppp) REVERT: C 465 MET cc_start: 0.7926 (mmt) cc_final: 0.7606 (mmt) outliers start: 31 outliers final: 23 residues processed: 216 average time/residue: 0.1183 time to fit residues: 37.8845 Evaluate side-chains 207 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 580 THR 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 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 352 ASP 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 206 TYR Chi-restraints excluded: chain C residue 268 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 164 optimal weight: 40.0000 chunk 109 optimal weight: 0.0770 chunk 4 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 HIS ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** 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 = 0.4103 r_free = 0.4103 target = 0.125873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.101762 restraints weight = 29216.419| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.88 r_work: 0.3559 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14425 Z= 0.165 Angle : 0.596 11.309 19725 Z= 0.306 Chirality : 0.041 0.275 2115 Planarity : 0.004 0.043 2389 Dihedral : 14.742 61.651 2242 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.11 % Allowed : 14.92 % Favored : 82.97 % 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 are not related in a simple way. whole: 0.44 (0.21), residues: 1604 helix: 1.16 (0.20), residues: 653 sheet: -0.64 (0.34), residues: 225 loop : -0.08 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 107 TYR 0.015 0.002 TYR C 291 PHE 0.048 0.002 PHE A 939 TRP 0.084 0.002 TRP A 896 HIS 0.011 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (14425) covalent geometry : angle 0.59605 / 0.31 (19725) hydrogen bonds : bond 0.03702 / 2.52 ( 635) hydrogen bonds : angle 4.90361 / 3.54 ( 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 219 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ILE cc_start: 0.8809 (mp) cc_final: 0.8558 (mp) REVERT: A 214 GLU cc_start: 0.8017 (tp30) cc_final: 0.7798 (tt0) REVERT: A 381 ASP cc_start: 0.8626 (m-30) cc_final: 0.8390 (t0) REVERT: A 922 GLU cc_start: 0.7780 (tp30) cc_final: 0.7266 (tp30) REVERT: A 1035 MET cc_start: 0.6997 (tmm) cc_final: 0.6365 (tmm) REVERT: B 301 GLU cc_start: 0.7975 (tp30) cc_final: 0.7628 (mm-30) REVERT: B 386 ASP cc_start: 0.7941 (t0) cc_final: 0.7613 (t0) REVERT: B 449 GLU cc_start: 0.7705 (mp0) cc_final: 0.7319 (mp0) REVERT: C 197 LEU cc_start: 0.4752 (OUTLIER) cc_final: 0.4433 (mt) REVERT: C 236 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6668 (mt-10) REVERT: C 278 CYS cc_start: 0.7210 (t) cc_final: 0.6790 (m) REVERT: C 291 TYR cc_start: 0.7900 (t80) cc_final: 0.7605 (t80) REVERT: C 301 GLU cc_start: 0.7344 (tt0) cc_final: 0.7115 (tt0) REVERT: C 313 HIS cc_start: 0.7455 (OUTLIER) cc_final: 0.7212 (p-80) REVERT: C 421 MET cc_start: 0.7358 (tmm) cc_final: 0.6975 (ppp) REVERT: C 465 MET cc_start: 0.7910 (mmt) cc_final: 0.7600 (mmt) outliers start: 30 outliers final: 21 residues processed: 211 average time/residue: 0.1169 time to fit residues: 36.8142 Evaluate side-chains 209 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU 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 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 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 347 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 104 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.0570 chunk 71 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 62 optimal weight: 0.0470 chunk 35 optimal weight: 0.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 HIS ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 323 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.127269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.102513 restraints weight = 29062.893| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.94 r_work: 0.3600 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14425 Z= 0.120 Angle : 0.589 14.047 19725 Z= 0.300 Chirality : 0.040 0.344 2115 Planarity : 0.004 0.042 2389 Dihedral : 14.673 61.283 2242 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.48 % Allowed : 16.12 % Favored : 82.41 % 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 are not related in a simple way. whole: 0.60 (0.22), residues: 1604 helix: 1.29 (0.21), residues: 657 sheet: -0.57 (0.35), residues: 225 loop : 0.02 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 344 TYR 0.016 0.001 TYR C 291 PHE 0.025 0.001 PHE A 939 TRP 0.088 0.002 TRP A 896 HIS 0.011 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (14425) covalent geometry : angle 0.58872 / 0.30 (19725) hydrogen bonds : bond 0.03469 / 2.36 ( 635) hydrogen bonds : angle 4.78886 / 3.45 ( 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 212 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.8012 (tp30) cc_final: 0.7808 (tt0) REVERT: A 381 ASP cc_start: 0.8587 (m-30) cc_final: 0.8354 (t0) REVERT: A 441 MET cc_start: 0.7868 (tmm) cc_final: 0.7503 (ttt) REVERT: A 855 MET cc_start: 0.8902 (mmm) cc_final: 0.8380 (mmm) REVERT: A 1035 MET cc_start: 0.6844 (tmm) cc_final: 0.6476 (tmm) REVERT: A 1141 MET cc_start: 0.7963 (tpt) cc_final: 0.7561 (tpp) REVERT: B 253 ASP cc_start: 0.8247 (t70) cc_final: 0.7989 (t0) REVERT: B 301 GLU cc_start: 0.7870 (tp30) cc_final: 0.7563 (mm-30) REVERT: B 386 ASP cc_start: 0.7929 (t0) cc_final: 0.7605 (t0) REVERT: B 449 GLU cc_start: 0.7685 (mp0) cc_final: 0.7368 (mp0) REVERT: B 465 MET cc_start: 0.7368 (mtt) cc_final: 0.7116 (mtt) REVERT: C 236 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6668 (mt-10) REVERT: C 278 CYS cc_start: 0.7227 (t) cc_final: 0.6791 (m) REVERT: C 291 TYR cc_start: 0.7857 (t80) cc_final: 0.7563 (t80) REVERT: C 301 GLU cc_start: 0.7299 (tt0) cc_final: 0.7052 (tt0) REVERT: C 313 HIS cc_start: 0.7482 (OUTLIER) cc_final: 0.7226 (p-80) REVERT: C 421 MET cc_start: 0.7398 (tmm) cc_final: 0.7044 (ppp) REVERT: C 465 MET cc_start: 0.7871 (mmt) cc_final: 0.7538 (mmt) outliers start: 21 outliers final: 16 residues processed: 207 average time/residue: 0.1216 time to fit residues: 36.8931 Evaluate side-chains 196 residues out of total 1422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU 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 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 383 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 104 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 90 optimal weight: 0.0570 chunk 76 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 17 optimal weight: 0.0370 chunk 96 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 HIS ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 323 HIS ** 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 = 0.4100 r_free = 0.4100 target = 0.125550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.101536 restraints weight = 29406.424| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.88 r_work: 0.3560 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14425 Z= 0.178 Angle : 0.623 14.978 19725 Z= 0.314 Chirality : 0.043 0.437 2115 Planarity : 0.004 0.044 2389 Dihedral : 14.710 61.663 2242 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.27 % Allowed : 16.75 % 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 are not related in a simple way. whole: 0.53 (0.21), residues: 1604 helix: 1.24 (0.20), residues: 653 sheet: -0.62 (0.35), residues: 225 loop : -0.02 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 458 TYR 0.015 0.002 TYR C 291 PHE 0.026 0.002 PHE A 939 TRP 0.074 0.002 TRP A 896 HIS 0.011 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (14425) covalent geometry : angle 0.62333 / 0.31 (19725) hydrogen bonds : bond 0.03731 / 2.54 ( 635) hydrogen bonds : angle 4.89907 / 3.53 ( 1750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2963.18 seconds wall clock time: 51 minutes 50.02 seconds (3110.02 seconds total)