Starting phenix.real_space_refine on Thu Aug 6 12:23:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8udl_42150/08_2026/8udl_42150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8udl_42150/08_2026/8udl_42150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8udl_42150/08_2026/8udl_42150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8udl_42150/08_2026/8udl_42150.map" model { file = "/net/cci-nas-00/data/ceres_data/8udl_42150/08_2026/8udl_42150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8udl_42150/08_2026/8udl_42150.cif" } resolution = 2.37 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= 0.366 sd= 0.630 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: 5 Type Number sf(0) Gaussians P 46 5.49 5 S 82 5.16 5 C 9579 2.51 5 N 2679 2.21 5 O 2859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15245 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7778 Classifications: {'peptide': 974} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 65, 'TRANS': 908} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3300 Classifications: {'peptide': 410} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3222 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 2 Chain: "P" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "T" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 494 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Time building chain proxies: 2.98, per 1000 atoms: 0.20 Number of scatterers: 15245 At special positions: 0 Unit cell: (115.24, 109.22, 153.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 46 15.00 O 2859 8.00 N 2679 7.00 C 9579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A1077 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 576.3 milliseconds 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 14 sheets defined 49.9% alpha, 13.5% beta 20 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 72 through 76 removed outlier: 4.287A pdb=" N ILE A 76 " --> pdb=" O PRO A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 96 through 111 removed outlier: 3.564A pdb=" N HIS A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 158 Proline residue: A 149 - end of helix removed outlier: 3.535A pdb=" N LEU A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 270 through 276 removed outlier: 4.094A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 6.653A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 305 through 315 removed outlier: 3.507A pdb=" N SER A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 removed outlier: 3.856A pdb=" N ASP A 349 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 351 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 removed outlier: 3.698A pdb=" N GLN A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.173A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 3.815A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 482 removed outlier: 3.680A pdb=" N SER A 475 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 478 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 554 Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.736A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 650 through 663 Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 786 through 810 removed outlier: 5.117A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 858 through 862 removed outlier: 3.563A pdb=" N ALA A 862 " --> pdb=" O TRP A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 878 removed outlier: 4.385A pdb=" N LYS A 875 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 923 Processing helix chain 'A' and resid 930 through 939 removed outlier: 3.544A pdb=" N VAL A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 955 removed outlier: 3.727A pdb=" N ILE A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 955 " --> pdb=" O TYR A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 974 through 990 Processing helix chain 'A' and resid 1054 through 1067 Processing helix chain 'A' and resid 1080 through 1084 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.798A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1168 removed outlier: 3.535A pdb=" N ALA A1150 " --> pdb=" O ARG A1146 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A1151 " --> pdb=" O TYR A1147 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1178 Processing helix chain 'A' and resid 1205 through 1210 Processing helix chain 'A' and resid 1219 through 1228 Processing helix chain 'B' and resid 65 through 76 Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.706A pdb=" N ARG B 154 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU B 155 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 156 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 4.027A pdb=" N VAL B 168 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.812A pdb=" N ASN B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 198 through 201 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: 4.024A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 3.716A 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 318 through 322 Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.685A pdb=" N PHE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 391 through 409 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 444 through 451 removed outlier: 3.833A pdb=" N LEU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 483 removed outlier: 3.941A pdb=" N LYS B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 150 through 157 removed outlier: 3.737A pdb=" N LEU C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.648A pdb=" N LEU C 162 " --> pdb=" O ASP C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 177 removed outlier: 4.327A pdb=" N LEU C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 172 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 191 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.409A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.634A pdb=" N LYS C 321 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.600A pdb=" N PHE C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 409 removed outlier: 3.814A pdb=" N GLN C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 removed outlier: 3.882A pdb=" N THR C 420 " --> pdb=" O TYR C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.614A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 484 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 186 removed outlier: 3.530A pdb=" N SER A 222 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 438 removed outlier: 3.674A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 748 through 751 Processing sheet with id=AA4, first strand: chain 'A' and resid 1127 through 1132 removed outlier: 6.763A pdb=" N ARG A1138 " --> pdb=" O CYS A1130 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A1132 " --> pdb=" O GLU A1136 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU A1136 " --> pdb=" O SER A1132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 991 through 992 Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.372A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR B 206 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL B 335 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN B 305 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 146 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 413 through 414 removed outlier: 7.092A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 125 through 127 removed outlier: 3.504A pdb=" N TYR C 206 " --> pdb=" O PHE C 242 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER C 230 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL C 335 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS C 285 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AB4, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB5, first strand: chain 'C' and resid 413 through 415 removed outlier: 6.839A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 442 " --> pdb=" O HIS C 454 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS C 454 " --> pdb=" O LEU C 442 " (cutoff:3.500A) 667 hydrogen bonds defined for protein. 1836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4499 1.34 - 1.46: 2950 1.46 - 1.58: 8058 1.58 - 1.70: 90 1.70 - 1.82: 128 Bond restraints: 15725 Sorted by residual: bond pdb=" C3' DG P 8 " pdb=" C2' DG P 8 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.20e+01 bond pdb=" C3' DC T 21 " pdb=" C2' DC T 21 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.90e+01 bond pdb=" C3' DC T 13 " pdb=" C2' DC T 13 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.89e+01 bond pdb=" C3' DT T 14 " pdb=" C2' DT T 14 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.45e+01 bond pdb=" C3' DC P 10 " pdb=" C2' DC P 10 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.40e+01 ... (remaining 15720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 20133 1.46 - 2.92: 1184 2.92 - 4.39: 153 4.39 - 5.85: 31 5.85 - 7.31: 5 Bond angle restraints: 21506 Sorted by residual: angle pdb=" O4' DT T 25 " pdb=" C4' DT T 25 " pdb=" C3' DT T 25 " ideal model delta sigma weight residual 106.00 102.30 3.70 6.00e-01 2.78e+00 3.81e+01 angle pdb=" N3 DT T 23 " pdb=" C4 DT T 23 " pdb=" O4 DT T 23 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT T 25 " pdb=" C4 DT T 25 " pdb=" O4 DT T 25 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT P 17 " pdb=" C4 DT P 17 " pdb=" O4 DT P 17 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT T 14 " pdb=" C4 DT T 14 " pdb=" O4 DT T 14 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 ... (remaining 21501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8289 17.90 - 35.80: 701 35.80 - 53.70: 201 53.70 - 71.60: 62 71.60 - 89.50: 13 Dihedral angle restraints: 9266 sinusoidal: 4122 harmonic: 5144 Sorted by residual: dihedral pdb=" CA GLY A 114 " pdb=" C GLY A 114 " pdb=" N GLN A 115 " pdb=" CA GLN A 115 " ideal model delta harmonic sigma weight residual -180.00 -151.39 -28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA GLY A 871 " pdb=" C GLY A 871 " pdb=" N SER A 872 " pdb=" CA SER A 872 " ideal model delta harmonic sigma weight residual -180.00 -152.61 -27.39 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA ARG B 203 " pdb=" C ARG B 203 " pdb=" N LEU B 204 " pdb=" CA LEU B 204 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 9263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1566 0.044 - 0.088: 528 0.088 - 0.132: 196 0.132 - 0.176: 26 0.176 - 0.220: 2 Chirality restraints: 2318 Sorted by residual: chirality pdb=" C4' DG P 8 " pdb=" C5' DG P 8 " pdb=" O4' DG P 8 " pdb=" C3' DG P 8 " both_signs ideal model delta sigma weight residual False -2.53 -2.31 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ASP A 868 " pdb=" N ASP A 868 " pdb=" C ASP A 868 " pdb=" CB ASP A 868 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C3' DG T 16 " pdb=" C4' DG T 16 " pdb=" O3' DG T 16 " pdb=" C2' DG T 16 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.46e-01 ... (remaining 2315 not shown) Planarity restraints: 2602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 259 " 0.306 9.50e-02 1.11e+02 1.38e-01 1.50e+01 pdb=" NE ARG B 259 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 259 " 0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG B 259 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 259 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 284 " -0.303 9.50e-02 1.11e+02 1.37e-01 1.37e+01 pdb=" NE ARG B 284 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG B 284 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG B 284 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B 284 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 102 " 0.266 9.50e-02 1.11e+02 1.20e-01 1.06e+01 pdb=" NE ARG A 102 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 102 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 102 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 102 " 0.002 2.00e-02 2.50e+03 ... (remaining 2599 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2794 2.79 - 3.31: 14021 3.31 - 3.84: 24157 3.84 - 4.37: 28463 4.37 - 4.90: 47619 Nonbonded interactions: 117054 Sorted by model distance: nonbonded pdb=" O THR C 444 " pdb=" OG1 THR C 447 " model vdw 2.257 3.040 nonbonded pdb=" O ASP B 142 " pdb=" NH2 ARG B 146 " model vdw 2.267 3.120 nonbonded pdb=" OD1 ASP B 142 " pdb=" NH2 ARG B 146 " model vdw 2.281 3.120 nonbonded pdb=" NE2 GLN B 158 " pdb=" OD1 ASP B 159 " model vdw 2.287 3.120 nonbonded pdb=" O SER A 593 " pdb=" OG1 THR A 599 " model vdw 2.291 3.040 ... (remaining 117049 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 219 or resid 228 through 355 or resid 368 throu \ gh 485)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.690 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 : 0.004 0.041 15726 Z= 0.272 Angle : 0.761 7.309 21508 Z= 0.496 Chirality : 0.050 0.220 2318 Planarity : 0.010 0.138 2602 Dihedral : 15.489 89.505 5943 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.81 % Favored : 96.07 % Rotamer: Outliers : 0.39 % Allowed : 3.42 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.19), residues: 1757 helix: -0.82 (0.17), residues: 769 sheet: 0.89 (0.31), residues: 242 loop : -0.47 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.003 ARG B 259 TYR 0.022 0.004 TYR C 432 PHE 0.029 0.002 PHE A 197 TRP 0.024 0.003 TRP A 572 HIS 0.007 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.27 (15725) covalent geometry : angle 0.76071 / 0.50 (21506) SS BOND : bond 0.00814 / 0.43 ( 1) SS BOND : angle 0.92466 / 0.52 ( 2) hydrogen bonds : bond 0.17806 / 12.29 ( 718) hydrogen bonds : angle 6.20254 / 4.26 ( 1938) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 523 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 HIS cc_start: 0.6996 (m170) cc_final: 0.6743 (m170) REVERT: A 616 GLU cc_start: 0.7270 (tp30) cc_final: 0.6813 (tp30) REVERT: A 1066 THR cc_start: 0.7873 (m) cc_final: 0.7619 (p) REVERT: B 64 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6141 (mm-30) REVERT: B 170 PHE cc_start: 0.6582 (t80) cc_final: 0.6380 (t80) REVERT: C 219 PHE cc_start: 0.6663 (OUTLIER) cc_final: 0.5756 (t80) outliers start: 6 outliers final: 2 residues processed: 528 average time/residue: 0.5197 time to fit residues: 300.6394 Evaluate side-chains 380 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 376 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 228 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 468 ASN A 493 GLN A 565 HIS A 945 HIS A 968 GLN B 74 GLN B 305 ASN B 404 ASN B 422 GLN C 74 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.138462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.130103 restraints weight = 25636.332| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.25 r_work: 0.3788 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15726 Z= 0.180 Angle : 0.747 9.626 21508 Z= 0.404 Chirality : 0.048 0.241 2318 Planarity : 0.006 0.066 2602 Dihedral : 14.695 59.736 2440 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 5.04 % Allowed : 13.94 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.20), residues: 1757 helix: 0.41 (0.19), residues: 773 sheet: 0.95 (0.32), residues: 232 loop : -0.19 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 972 TYR 0.019 0.002 TYR A1108 PHE 0.023 0.002 PHE A 197 TRP 0.017 0.002 TRP A 897 HIS 0.006 0.001 HIS A 945 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (15725) covalent geometry : angle 0.74658 / 0.40 (21506) SS BOND : bond 0.00743 / 0.39 ( 1) SS BOND : angle 0.86735 / 0.49 ( 2) hydrogen bonds : bond 0.07028 / 4.82 ( 718) hydrogen bonds : angle 5.13479 / 3.57 ( 1938) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 374 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8450 (tt) REVERT: A 361 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7337 (tmm160) REVERT: A 603 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.8021 (mtt) REVERT: A 1175 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6268 (tm-30) REVERT: B 219 PHE cc_start: 0.6459 (OUTLIER) cc_final: 0.5439 (p90) REVERT: C 219 PHE cc_start: 0.6689 (OUTLIER) cc_final: 0.5874 (t80) outliers start: 78 outliers final: 28 residues processed: 417 average time/residue: 0.4874 time to fit residues: 224.4321 Evaluate side-chains 374 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 340 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 HIS A 106 HIS A 281 GLN A 354 ASN A 945 HIS A1110 HIS B 74 GLN B 305 ASN B 422 GLN C 74 GLN C 258 HIS C 305 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.133406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.125176 restraints weight = 25773.883| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.23 r_work: 0.3721 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 15726 Z= 0.279 Angle : 0.876 11.793 21508 Z= 0.472 Chirality : 0.055 0.260 2318 Planarity : 0.008 0.083 2602 Dihedral : 14.942 59.857 2435 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.62 % Rotamer: Outliers : 6.33 % Allowed : 16.66 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.20), residues: 1757 helix: 0.10 (0.18), residues: 779 sheet: 0.58 (0.30), residues: 245 loop : -0.73 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 443 TYR 0.024 0.003 TYR A1108 PHE 0.027 0.003 PHE A 197 TRP 0.019 0.003 TRP A 897 HIS 0.008 0.002 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.28 (15725) covalent geometry : angle 0.87565 / 0.47 (21506) SS BOND : bond 0.00999 / 0.53 ( 1) SS BOND : angle 1.18239 / 0.67 ( 2) hydrogen bonds : bond 0.09015 / 6.20 ( 718) hydrogen bonds : angle 5.22829 / 3.65 ( 1938) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 356 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 361 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7486 (tmm160) REVERT: A 456 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: A 603 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.8046 (mtt) REVERT: A 994 TRP cc_start: 0.4358 (OUTLIER) cc_final: 0.2418 (m100) REVERT: A 1175 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.6429 (tm-30) REVERT: B 134 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7707 (mptt) REVERT: B 445 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6161 (pm20) REVERT: C 202 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7467 (mtmt) REVERT: C 219 PHE cc_start: 0.6938 (OUTLIER) cc_final: 0.6129 (t80) REVERT: C 236 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: C 445 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6786 (pp20) outliers start: 98 outliers final: 50 residues processed: 410 average time/residue: 0.5065 time to fit residues: 229.6244 Evaluate side-chains 394 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 333 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 977 GLU Chi-restraints excluded: chain A residue 990 LYS Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1142 ARG Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 261 GLN Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 151 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 550 GLN ** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 258 HIS B 305 ASN B 404 ASN C 74 GLN ** C 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.135569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.127399 restraints weight = 26046.121| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.24 r_work: 0.3754 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15726 Z= 0.171 Angle : 0.712 8.560 21508 Z= 0.384 Chirality : 0.047 0.242 2318 Planarity : 0.006 0.077 2602 Dihedral : 14.787 59.936 2435 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.75 % Allowed : 18.59 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.16 (0.20), residues: 1757 helix: 0.63 (0.19), residues: 763 sheet: 0.70 (0.30), residues: 241 loop : -0.55 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 443 TYR 0.018 0.002 TYR C 432 PHE 0.018 0.002 PHE A 197 TRP 0.021 0.002 TRP B 304 HIS 0.006 0.001 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (15725) covalent geometry : angle 0.71163 / 0.38 (21506) SS BOND : bond 0.00619 / 0.33 ( 1) SS BOND : angle 0.98077 / 0.56 ( 2) hydrogen bonds : bond 0.06896 / 4.79 ( 718) hydrogen bonds : angle 4.92601 / 3.43 ( 1938) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 351 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 361 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7364 (tmm160) REVERT: A 456 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: A 603 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.8028 (mtt) REVERT: A 994 TRP cc_start: 0.4268 (OUTLIER) cc_final: 0.2428 (t-100) REVERT: A 1175 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.6473 (tm-30) REVERT: B 219 PHE cc_start: 0.6512 (OUTLIER) cc_final: 0.5405 (p90) REVERT: B 347 LEU cc_start: 0.8454 (tp) cc_final: 0.8213 (tm) REVERT: C 219 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.6098 (t80) REVERT: C 445 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6725 (pm20) outliers start: 89 outliers final: 42 residues processed: 404 average time/residue: 0.4745 time to fit residues: 212.3751 Evaluate side-chains 384 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 334 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1063 SER Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1136 GLU Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 50 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 550 GLN A 618 HIS A 968 GLN B 74 GLN B 258 HIS B 305 ASN C 74 GLN C 309 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.136930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.128760 restraints weight = 25900.836| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.25 r_work: 0.3772 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15726 Z= 0.149 Angle : 0.673 7.906 21508 Z= 0.358 Chirality : 0.045 0.272 2318 Planarity : 0.005 0.066 2602 Dihedral : 14.703 59.817 2435 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.42 % Allowed : 18.92 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.20), residues: 1757 helix: 0.92 (0.19), residues: 760 sheet: 0.78 (0.31), residues: 239 loop : -0.47 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 443 TYR 0.022 0.002 TYR C 432 PHE 0.015 0.001 PHE A 197 TRP 0.018 0.002 TRP B 241 HIS 0.012 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (15725) covalent geometry : angle 0.67263 / 0.36 (21506) SS BOND : bond 0.00509 / 0.27 ( 1) SS BOND : angle 0.90193 / 0.52 ( 2) hydrogen bonds : bond 0.06062 / 4.25 ( 718) hydrogen bonds : angle 4.75131 / 3.31 ( 1938) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 341 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7308 (tmm160) REVERT: A 456 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7603 (mm-40) REVERT: A 603 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.8038 (mtt) REVERT: A 994 TRP cc_start: 0.4267 (OUTLIER) cc_final: 0.2459 (t-100) REVERT: A 1175 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6504 (tm-30) REVERT: B 134 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7647 (mptt) REVERT: B 219 PHE cc_start: 0.6452 (OUTLIER) cc_final: 0.5406 (p90) REVERT: B 344 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7019 (ttt180) REVERT: B 347 LEU cc_start: 0.8443 (tp) cc_final: 0.8210 (tm) REVERT: C 202 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7351 (mtmt) REVERT: C 219 PHE cc_start: 0.6924 (OUTLIER) cc_final: 0.6078 (t80) REVERT: C 236 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: C 445 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6738 (pm20) outliers start: 84 outliers final: 35 residues processed: 388 average time/residue: 0.4702 time to fit residues: 202.5285 Evaluate side-chains 378 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 331 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1142 ARG Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 444 THR Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 9 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 chunk 147 optimal weight: 0.1980 chunk 161 optimal weight: 9.9990 chunk 96 optimal weight: 0.5980 chunk 120 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 569 HIS A1157 ASN B 74 GLN B 305 ASN B 404 ASN C 74 GLN C 309 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.137552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.129397 restraints weight = 25958.487| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.25 r_work: 0.3782 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15726 Z= 0.141 Angle : 0.659 11.047 21508 Z= 0.347 Chirality : 0.044 0.291 2318 Planarity : 0.005 0.061 2602 Dihedral : 14.650 59.995 2435 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.97 % Allowed : 19.95 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.20), residues: 1757 helix: 1.01 (0.19), residues: 761 sheet: 0.91 (0.31), residues: 244 loop : -0.44 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 443 TYR 0.024 0.002 TYR C 432 PHE 0.019 0.001 PHE C 170 TRP 0.024 0.002 TRP B 241 HIS 0.011 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (15725) covalent geometry : angle 0.65875 / 0.35 (21506) SS BOND : bond 0.00475 / 0.25 ( 1) SS BOND : angle 0.85177 / 0.49 ( 2) hydrogen bonds : bond 0.05695 / 4.00 ( 718) hydrogen bonds : angle 4.66395 / 3.25 ( 1938) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 332 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 361 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7229 (tmm160) REVERT: A 374 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7225 (ptm160) REVERT: A 456 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7582 (mm-40) REVERT: A 860 LEU cc_start: 0.8585 (mm) cc_final: 0.8362 (tm) REVERT: A 994 TRP cc_start: 0.4248 (OUTLIER) cc_final: 0.2439 (t-100) REVERT: A 1175 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6538 (tm-30) REVERT: B 134 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7667 (mptt) REVERT: B 219 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.5346 (p90) REVERT: B 321 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7159 (tptt) REVERT: B 347 LEU cc_start: 0.8413 (tp) cc_final: 0.8189 (tm) REVERT: C 219 PHE cc_start: 0.6962 (OUTLIER) cc_final: 0.6099 (t80) REVERT: C 445 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6667 (pm20) outliers start: 77 outliers final: 37 residues processed: 378 average time/residue: 0.4873 time to fit residues: 203.7372 Evaluate side-chains 369 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 322 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 892 ASP Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1142 ARG Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 22 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 HIS A 864 ASN B 74 GLN B 292 ASN B 305 ASN B 400 GLN C 74 GLN C 309 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.133718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.125609 restraints weight = 25744.518| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.23 r_work: 0.3728 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15726 Z= 0.238 Angle : 0.804 9.856 21508 Z= 0.425 Chirality : 0.052 0.292 2318 Planarity : 0.007 0.066 2602 Dihedral : 14.803 59.368 2434 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.87 % Allowed : 20.01 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.03 (0.20), residues: 1757 helix: 0.61 (0.19), residues: 757 sheet: 0.47 (0.31), residues: 236 loop : -0.65 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 443 TYR 0.032 0.003 TYR C 432 PHE 0.022 0.003 PHE A 197 TRP 0.024 0.002 TRP B 241 HIS 0.009 0.002 HIS C 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 (15725) covalent geometry : angle 0.80365 / 0.42 (21506) SS BOND : bond 0.00869 / 0.46 ( 1) SS BOND : angle 1.19909 / 0.66 ( 2) hydrogen bonds : bond 0.07874 / 5.46 ( 718) hydrogen bonds : angle 5.00552 / 3.49 ( 1938) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 326 time to evaluate : 0.519 Fit side-chains REVERT: A 361 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7303 (tmm160) REVERT: A 374 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7250 (ptm160) REVERT: A 456 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7675 (tt0) REVERT: A 478 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7135 (mtp85) REVERT: A 994 TRP cc_start: 0.4463 (OUTLIER) cc_final: 0.2569 (t-100) REVERT: A 1175 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.6522 (tm-30) REVERT: B 134 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7680 (mptt) REVERT: B 146 ARG cc_start: 0.7974 (mpt180) cc_final: 0.7409 (mmp-170) REVERT: B 321 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7248 (tptt) REVERT: B 344 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7097 (ttt180) REVERT: B 347 LEU cc_start: 0.8488 (tp) cc_final: 0.8248 (tm) REVERT: B 389 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.5683 (ppt170) REVERT: C 202 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7475 (mtmt) REVERT: C 219 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.6136 (t80) REVERT: C 236 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: C 445 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6687 (pp20) outliers start: 91 outliers final: 39 residues processed: 380 average time/residue: 0.4829 time to fit residues: 202.6738 Evaluate side-chains 372 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 319 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 107 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 569 HIS A 663 GLN B 74 GLN B 258 HIS B 305 ASN C 74 GLN C 309 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.136677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.128651 restraints weight = 26004.013| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.24 r_work: 0.3774 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15726 Z= 0.144 Angle : 0.682 10.533 21508 Z= 0.357 Chirality : 0.045 0.341 2318 Planarity : 0.005 0.057 2602 Dihedral : 14.693 59.992 2434 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.26 % Allowed : 21.95 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.20), residues: 1757 helix: 0.90 (0.19), residues: 757 sheet: 0.81 (0.32), residues: 230 loop : -0.53 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 443 TYR 0.030 0.002 TYR C 432 PHE 0.016 0.001 PHE A 961 TRP 0.022 0.001 TRP B 241 HIS 0.012 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (15725) covalent geometry : angle 0.68190 / 0.36 (21506) SS BOND : bond 0.00495 / 0.26 ( 1) SS BOND : angle 0.79595 / 0.46 ( 2) hydrogen bonds : bond 0.05870 / 4.13 ( 718) hydrogen bonds : angle 4.72031 / 3.29 ( 1938) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 334 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 361 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7225 (tmm160) REVERT: A 374 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7164 (ptm160) REVERT: A 456 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: A 478 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7087 (mtp85) REVERT: A 658 LYS cc_start: 0.7994 (tmmt) cc_final: 0.7570 (ttpt) REVERT: A 994 TRP cc_start: 0.4200 (OUTLIER) cc_final: 0.2353 (t-100) REVERT: A 1175 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6549 (tm-30) REVERT: B 134 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7661 (mptt) REVERT: B 219 PHE cc_start: 0.6486 (OUTLIER) cc_final: 0.5302 (p90) REVERT: B 321 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.7201 (tptt) REVERT: B 344 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7052 (ttt180) REVERT: B 347 LEU cc_start: 0.8417 (tp) cc_final: 0.8201 (tm) REVERT: B 389 ARG cc_start: 0.6202 (OUTLIER) cc_final: 0.5758 (ppt170) REVERT: B 400 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7225 (tm-30) REVERT: C 202 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7402 (mtmt) REVERT: C 219 PHE cc_start: 0.6984 (OUTLIER) cc_final: 0.6118 (t80) REVERT: C 445 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6541 (pp20) outliers start: 66 outliers final: 29 residues processed: 376 average time/residue: 0.5533 time to fit residues: 229.7171 Evaluate side-chains 370 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 326 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 977 GLU Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 142 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 157 optimal weight: 0.1980 chunk 40 optimal weight: 0.0980 chunk 48 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 HIS A 663 GLN B 74 GLN B 305 ASN C 74 GLN C 309 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.136982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.128904 restraints weight = 25949.709| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.24 r_work: 0.3779 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15726 Z= 0.143 Angle : 0.676 10.569 21508 Z= 0.354 Chirality : 0.045 0.344 2318 Planarity : 0.005 0.055 2602 Dihedral : 14.667 59.724 2434 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.94 % Allowed : 22.85 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.20), residues: 1757 helix: 1.01 (0.19), residues: 752 sheet: 0.83 (0.32), residues: 235 loop : -0.46 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 443 TYR 0.016 0.001 TYR A1108 PHE 0.014 0.001 PHE A 961 TRP 0.023 0.001 TRP B 241 HIS 0.012 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (15725) covalent geometry : angle 0.67639 / 0.35 (21506) SS BOND : bond 0.00476 / 0.25 ( 1) SS BOND : angle 0.81217 / 0.46 ( 2) hydrogen bonds : bond 0.05715 / 4.02 ( 718) hydrogen bonds : angle 4.67649 / 3.26 ( 1938) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 329 time to evaluate : 0.577 Fit side-chains REVERT: A 361 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7575 (ttm170) REVERT: A 374 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7188 (ptm160) REVERT: A 456 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: A 478 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7073 (mtp85) REVERT: A 658 LYS cc_start: 0.7993 (tmmt) cc_final: 0.7604 (ttpt) REVERT: A 977 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: A 994 TRP cc_start: 0.4215 (OUTLIER) cc_final: 0.2375 (t-100) REVERT: A 1175 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.6510 (tm-30) REVERT: B 134 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7665 (mptt) REVERT: B 219 PHE cc_start: 0.6467 (OUTLIER) cc_final: 0.5329 (p90) REVERT: B 344 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7045 (ttt180) REVERT: B 347 LEU cc_start: 0.8419 (tp) cc_final: 0.8200 (tm) REVERT: B 389 ARG cc_start: 0.6242 (OUTLIER) cc_final: 0.5797 (ppt170) REVERT: B 400 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: C 202 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7335 (mtmt) REVERT: C 219 PHE cc_start: 0.6976 (OUTLIER) cc_final: 0.6034 (t80) REVERT: C 445 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6742 (pm20) outliers start: 61 outliers final: 29 residues processed: 368 average time/residue: 0.5423 time to fit residues: 220.2131 Evaluate side-chains 367 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 323 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 977 GLU Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 62 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 85 optimal weight: 0.2980 chunk 34 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 550 GLN A 565 HIS A 569 HIS B 74 GLN B 305 ASN C 74 GLN C 309 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.134710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.126650 restraints weight = 26038.494| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.24 r_work: 0.3744 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15726 Z= 0.199 Angle : 0.765 10.019 21508 Z= 0.402 Chirality : 0.049 0.309 2318 Planarity : 0.006 0.060 2602 Dihedral : 14.759 59.320 2434 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.68 % Allowed : 23.50 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.13 (0.20), residues: 1757 helix: 0.70 (0.19), residues: 765 sheet: 0.53 (0.31), residues: 238 loop : -0.62 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 443 TYR 0.037 0.002 TYR C 432 PHE 0.021 0.002 PHE A 961 TRP 0.019 0.002 TRP B 241 HIS 0.010 0.002 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (15725) covalent geometry : angle 0.76521 / 0.40 (21506) SS BOND : bond 0.00713 / 0.38 ( 1) SS BOND : angle 1.10373 / 0.61 ( 2) hydrogen bonds : bond 0.07021 / 4.89 ( 718) hydrogen bonds : angle 4.86865 / 3.39 ( 1938) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 324 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 165 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7180 (ptpp) REVERT: A 361 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7236 (tmm160) REVERT: A 374 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7225 (ptm160) REVERT: A 456 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: A 994 TRP cc_start: 0.4404 (OUTLIER) cc_final: 0.2487 (t-100) REVERT: A 1175 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.6492 (tm-30) REVERT: B 134 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7676 (mptt) REVERT: B 344 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7057 (ttt180) REVERT: B 347 LEU cc_start: 0.8483 (tp) cc_final: 0.8258 (tm) REVERT: B 389 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5787 (ppt170) REVERT: B 400 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7290 (tm-30) REVERT: C 67 GLU cc_start: 0.6014 (pm20) cc_final: 0.5470 (pm20) REVERT: C 202 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7460 (mtmt) REVERT: C 219 PHE cc_start: 0.6973 (OUTLIER) cc_final: 0.6085 (t80) REVERT: C 236 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: C 445 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6599 (pp20) REVERT: C 465 MET cc_start: 0.7064 (tpp) cc_final: 0.6599 (mpp) outliers start: 57 outliers final: 34 residues processed: 362 average time/residue: 0.5394 time to fit residues: 215.8761 Evaluate side-chains 371 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 323 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 872 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 445 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 21 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 40 optimal weight: 0.0770 chunk 59 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 180 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 550 GLN A 569 HIS B 74 GLN B 305 ASN C 74 GLN C 309 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.136066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.128055 restraints weight = 25658.407| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.23 r_work: 0.3766 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3689 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15726 Z= 0.159 Angle : 0.715 10.360 21508 Z= 0.374 Chirality : 0.046 0.328 2318 Planarity : 0.005 0.057 2602 Dihedral : 14.709 59.655 2434 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.87 % Allowed : 23.37 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.20), residues: 1757 helix: 0.85 (0.19), residues: 760 sheet: 0.68 (0.32), residues: 235 loop : -0.56 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 443 TYR 0.038 0.002 TYR C 432 PHE 0.023 0.002 PHE A 969 TRP 0.020 0.002 TRP B 241 HIS 0.012 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (15725) covalent geometry : angle 0.71470 / 0.37 (21506) SS BOND : bond 0.00555 / 0.29 ( 1) SS BOND : angle 0.86545 / 0.49 ( 2) hydrogen bonds : bond 0.06152 / 4.30 ( 718) hydrogen bonds : angle 4.76639 / 3.32 ( 1938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6027.93 seconds wall clock time: 102 minutes 58.40 seconds (6178.40 seconds total)