Starting phenix.real_space_refine on Sat May 17 04:04:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8udl_42150/05_2025/8udl_42150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8udl_42150/05_2025/8udl_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_42150/05_2025/8udl_42150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8udl_42150/05_2025/8udl_42150.map" model { file = "/net/cci-nas-00/data/ceres_data/8udl_42150/05_2025/8udl_42150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8udl_42150/05_2025/8udl_42150.cif" } resolution = 2.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.91, per 1000 atoms: 0.58 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: 3.52 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 4.71 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: 5.87 Time building geometry restraints manager: 4.08 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=" C4' DG P 8 " pdb=" O4' DG P 8 " ideal model delta sigma weight residual 1.450 1.416 0.034 2.00e-02 2.50e+03 2.90e+00 bond pdb=" C3' DG P 8 " pdb=" C2' DG P 8 " ideal model delta sigma weight residual 1.525 1.554 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C4' DT T 25 " pdb=" O4' DT T 25 " ideal model delta sigma weight residual 1.450 1.422 0.028 2.00e-02 2.50e+03 1.89e+00 bond pdb=" C3' DC T 21 " pdb=" C2' DC T 21 " ideal model delta sigma weight residual 1.525 1.551 -0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" C3' DC T 13 " pdb=" C2' DC T 13 " ideal model delta sigma weight residual 1.525 1.551 -0.026 2.00e-02 2.50e+03 1.66e+00 ... (remaining 15720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 20213 1.46 - 2.92: 1140 2.92 - 4.39: 123 4.39 - 5.85: 25 5.85 - 7.31: 5 Bond angle restraints: 21506 Sorted by residual: angle pdb=" N LEU B 204 " pdb=" CA LEU B 204 " pdb=" C LEU B 204 " ideal model delta sigma weight residual 109.81 117.12 -7.31 2.21e+00 2.05e-01 1.09e+01 angle pdb=" C ILE A1133 " pdb=" N HIS A1134 " pdb=" CA HIS A1134 " ideal model delta sigma weight residual 121.54 127.13 -5.59 1.91e+00 2.74e-01 8.56e+00 angle pdb=" C TRP A 994 " pdb=" N TYR A 995 " pdb=" CA TYR A 995 " ideal model delta sigma weight residual 121.52 127.83 -6.31 2.34e+00 1.83e-01 7.28e+00 angle pdb=" N PHE A 389 " pdb=" CA PHE A 389 " pdb=" C PHE A 389 " ideal model delta sigma weight residual 111.02 114.30 -3.28 1.22e+00 6.72e-01 7.24e+00 angle pdb=" C2' DG P 8 " pdb=" C1' DG P 8 " pdb=" N9 DG P 8 " ideal model delta sigma weight residual 113.50 117.51 -4.01 1.50e+00 4.44e-01 7.16e+00 ... (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 - 0.043: 1563 0.043 - 0.086: 541 0.086 - 0.128: 186 0.128 - 0.171: 26 0.171 - 0.214: 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 -0.21 2.00e-01 2.50e+01 1.14e+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=" C1' DT P 22 " pdb=" O4' DT P 22 " pdb=" C2' DT P 22 " pdb=" N1 DT P 22 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 6.94e-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: 1.350 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: 0.690 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 37.290 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 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:9.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15726 Z= 0.170 Angle : 0.736 7.309 21508 Z= 0.436 Chirality : 0.048 0.214 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.003 TRP A 572 HIS 0.007 0.001 HIS C 258 PHE 0.029 0.002 PHE A 197 TYR 0.022 0.004 TYR C 432 ARG 0.032 0.003 ARG B 259 Details of bonding type rmsd hydrogen bonds : bond 0.17806 ( 718) hydrogen bonds : angle 6.20254 ( 1938) SS BOND : bond 0.00814 ( 1) SS BOND : angle 0.92466 ( 2) covalent geometry : bond 0.00323 (15725) covalent geometry : angle 0.73641 (21506) *********************** 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 : 1.810 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: 1.2670 time to fit residues: 735.0800 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 : 1.554 ------------------------------------------------------------------------------- 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 152 optimal weight: 3.9990 chunk 137 optimal weight: 0.3980 chunk 76 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 54 optimal weight: 0.0980 chunk 86 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 281 GLN A 468 ASN A 493 GLN A 565 HIS A 945 HIS A 968 GLN A1110 HIS B 74 GLN B 305 ASN B 404 ASN C 74 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.136618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.128312 restraints weight = 25625.529| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.24 r_work: 0.3763 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15726 Z= 0.205 Angle : 0.767 11.196 21508 Z= 0.414 Chirality : 0.048 0.206 2318 Planarity : 0.006 0.064 2602 Dihedral : 14.628 59.974 2440 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Rotamer: Outliers : 5.36 % Allowed : 14.27 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1757 helix: 0.32 (0.19), residues: 777 sheet: 0.92 (0.31), residues: 241 loop : -0.29 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 241 HIS 0.007 0.002 HIS B 467 PHE 0.026 0.002 PHE A 197 TYR 0.023 0.002 TYR A1108 ARG 0.010 0.001 ARG A 827 Details of bonding type rmsd hydrogen bonds : bond 0.07456 ( 718) hydrogen bonds : angle 5.10754 ( 1938) SS BOND : bond 0.00829 ( 1) SS BOND : angle 0.94009 ( 2) covalent geometry : bond 0.00445 (15725) covalent geometry : angle 0.76654 (21506) *********************** 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 455 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 372 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7387 (tmm160) REVERT: A 603 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7996 (mtt) REVERT: A 1175 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.6362 (tm-30) REVERT: B 219 PHE cc_start: 0.6533 (OUTLIER) cc_final: 0.5434 (p90) REVERT: C 219 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.5977 (t80) REVERT: C 236 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: C 389 ARG cc_start: 0.5206 (OUTLIER) cc_final: 0.5003 (tmm-80) REVERT: C 449 GLU cc_start: 0.6856 (tt0) cc_final: 0.6653 (tt0) outliers start: 83 outliers final: 27 residues processed: 416 average time/residue: 1.2407 time to fit residues: 568.7996 Evaluate side-chains 375 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 341 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 403 THR 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 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 219 PHE Chi-restraints excluded: chain B residue 425 LEU 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 236 GLU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 389 ARG 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 27 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 109 optimal weight: 0.4980 chunk 174 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 106 HIS A 468 ASN ** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 305 ASN C 74 GLN C 258 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.134229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.126059 restraints weight = 25654.691| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.23 r_work: 0.3732 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15726 Z= 0.231 Angle : 0.781 9.800 21508 Z= 0.422 Chirality : 0.049 0.208 2318 Planarity : 0.007 0.072 2602 Dihedral : 14.673 59.668 2435 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 6.78 % Allowed : 15.88 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1757 helix: 0.34 (0.19), residues: 773 sheet: 0.61 (0.30), residues: 245 loop : -0.61 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 241 HIS 0.006 0.002 HIS A 659 PHE 0.024 0.003 PHE A 197 TYR 0.022 0.003 TYR A1108 ARG 0.008 0.001 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.07876 ( 718) hydrogen bonds : angle 5.06037 ( 1938) SS BOND : bond 0.00877 ( 1) SS BOND : angle 1.07676 ( 2) covalent geometry : bond 0.00511 (15725) covalent geometry : angle 0.78106 (21506) *********************** 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 460 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 355 time to evaluate : 1.755 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6426 (tm-30) REVERT: A 361 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7464 (tmm160) REVERT: A 456 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: A 603 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.8013 (mtt) REVERT: A 994 TRP cc_start: 0.4570 (OUTLIER) cc_final: 0.2723 (t-100) REVERT: A 1175 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.6488 (tm-30) REVERT: B 134 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7690 (mptt) REVERT: B 219 PHE cc_start: 0.6595 (OUTLIER) cc_final: 0.5512 (p90) REVERT: C 202 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7451 (mtmt) REVERT: C 219 PHE cc_start: 0.6990 (OUTLIER) cc_final: 0.6146 (t80) REVERT: C 236 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: C 445 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6901 (pm20) outliers start: 105 outliers final: 49 residues processed: 417 average time/residue: 1.2286 time to fit residues: 564.7803 Evaluate side-chains 399 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 338 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 152 GLU 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 442 GLU 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 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 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 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 1204 THR Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 425 LEU 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 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 398 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 437 ILE 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 111 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 468 ASN A 550 GLN A 618 HIS B 74 GLN B 305 ASN B 404 ASN C 74 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.136202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.128086 restraints weight = 25766.518| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.24 r_work: 0.3762 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15726 Z= 0.162 Angle : 0.679 8.036 21508 Z= 0.363 Chirality : 0.044 0.222 2318 Planarity : 0.006 0.065 2602 Dihedral : 14.554 59.998 2435 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.36 % Allowed : 18.14 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1757 helix: 0.76 (0.19), residues: 761 sheet: 0.87 (0.31), residues: 233 loop : -0.46 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 304 HIS 0.008 0.001 HIS C 258 PHE 0.017 0.002 PHE A 197 TYR 0.018 0.002 TYR A1108 ARG 0.008 0.001 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.06288 ( 718) hydrogen bonds : angle 4.79420 ( 1938) SS BOND : bond 0.00563 ( 1) SS BOND : angle 0.85905 ( 2) covalent geometry : bond 0.00349 (15725) covalent geometry : angle 0.67857 (21506) *********************** 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 432 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 349 time to evaluate : 1.687 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6419 (tm-30) REVERT: A 361 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7348 (tmm160) REVERT: A 456 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7592 (mm-40) REVERT: A 994 TRP cc_start: 0.4071 (OUTLIER) cc_final: 0.2564 (t-100) REVERT: A 1175 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6485 (tm-30) REVERT: B 134 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7650 (mptt) REVERT: B 219 PHE cc_start: 0.6448 (OUTLIER) cc_final: 0.5382 (p90) REVERT: B 347 LEU cc_start: 0.8428 (tp) cc_final: 0.8199 (tm) REVERT: C 219 PHE cc_start: 0.6974 (OUTLIER) cc_final: 0.6124 (t80) outliers start: 83 outliers final: 33 residues processed: 393 average time/residue: 1.1388 time to fit residues: 495.8595 Evaluate side-chains 377 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 336 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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 152 GLU 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 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 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 1136 GLU 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 134 LYS Chi-restraints excluded: chain B residue 219 PHE 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 252 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 398 VAL 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 98 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 90 optimal weight: 0.0770 chunk 147 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 164 optimal weight: 20.0000 overall best weight: 2.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A 550 GLN A 569 HIS 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 = 0.3946 r_free = 0.3946 target = 0.136150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.128040 restraints weight = 26168.428| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.25 r_work: 0.3764 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15726 Z= 0.159 Angle : 0.671 8.542 21508 Z= 0.356 Chirality : 0.044 0.254 2318 Planarity : 0.006 0.063 2602 Dihedral : 14.502 59.683 2435 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.42 % Allowed : 18.79 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1757 helix: 0.86 (0.19), residues: 766 sheet: 0.80 (0.32), residues: 229 loop : -0.41 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 241 HIS 0.007 0.001 HIS C 309 PHE 0.016 0.002 PHE A 197 TYR 0.021 0.002 TYR C 432 ARG 0.009 0.001 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.06091 ( 718) hydrogen bonds : angle 4.69497 ( 1938) SS BOND : bond 0.00560 ( 1) SS BOND : angle 0.93010 ( 2) covalent geometry : bond 0.00346 (15725) covalent geometry : angle 0.67110 (21506) *********************** 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 429 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 345 time to evaluate : 1.753 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6418 (tm-30) REVERT: A 361 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7267 (tmm160) REVERT: A 456 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7596 (mm-40) REVERT: A 478 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7077 (mtp85) REVERT: A 994 TRP cc_start: 0.4113 (OUTLIER) cc_final: 0.2319 (t-100) REVERT: A 1175 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6504 (tm-30) REVERT: B 134 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7652 (mptt) REVERT: B 170 PHE cc_start: 0.6538 (OUTLIER) cc_final: 0.6038 (t80) REVERT: B 219 PHE cc_start: 0.6504 (OUTLIER) cc_final: 0.5341 (p90) REVERT: B 347 LEU cc_start: 0.8450 (tp) cc_final: 0.8218 (tm) REVERT: C 202 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7411 (mtmt) REVERT: C 219 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.6108 (t80) outliers start: 84 outliers final: 41 residues processed: 391 average time/residue: 1.1611 time to fit residues: 503.4543 Evaluate side-chains 380 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 328 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 152 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 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 464 MET 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 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 938 THR 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 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 1193 VAL Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 219 PHE 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 252 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 398 VAL 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 165 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 chunk 114 optimal weight: 0.7980 chunk 180 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 ASN A 569 HIS 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 = 0.3994 r_free = 0.3994 target = 0.139770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.131643 restraints weight = 26157.561| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.25 r_work: 0.3815 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3738 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3519 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= 0.122 Angle : 0.613 9.541 21508 Z= 0.318 Chirality : 0.041 0.271 2318 Planarity : 0.005 0.054 2602 Dihedral : 14.312 59.973 2434 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.07 % Allowed : 20.72 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.20), residues: 1757 helix: 1.17 (0.20), residues: 758 sheet: 0.94 (0.31), residues: 248 loop : -0.26 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 241 HIS 0.011 0.001 HIS C 309 PHE 0.019 0.001 PHE C 170 TYR 0.020 0.001 TYR C 432 ARG 0.009 0.000 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 718) hydrogen bonds : angle 4.44081 ( 1938) SS BOND : bond 0.00341 ( 1) SS BOND : angle 0.68435 ( 2) covalent geometry : bond 0.00255 (15725) covalent geometry : angle 0.61324 (21506) *********************** 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 415 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 352 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6331 (tm-30) REVERT: A 456 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: A 478 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7021 (mtp85) REVERT: A 658 LYS cc_start: 0.7973 (tmmt) cc_final: 0.7671 (ttpt) REVERT: A 994 TRP cc_start: 0.4067 (OUTLIER) cc_final: 0.2114 (m100) REVERT: B 170 PHE cc_start: 0.6473 (OUTLIER) cc_final: 0.5868 (t80) REVERT: B 219 PHE cc_start: 0.6420 (OUTLIER) cc_final: 0.5310 (p90) REVERT: B 347 LEU cc_start: 0.8350 (tp) cc_final: 0.8129 (tm) REVERT: C 219 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.6005 (t80) REVERT: C 479 ILE cc_start: 0.8169 (mm) cc_final: 0.7950 (tp) outliers start: 63 outliers final: 26 residues processed: 392 average time/residue: 1.1528 time to fit residues: 499.6373 Evaluate side-chains 361 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 328 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 305 SER 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 464 MET 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 902 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 977 GLU Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1142 ARG Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 219 PHE 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 393 LEU 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 179 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 HIS A 864 ASN A 968 GLN A1134 HIS B 74 GLN B 84 GLN B 158 GLN B 305 ASN C 74 GLN C 96 HIS C 305 ASN C 323 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.132194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.124101 restraints weight = 25880.507| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.23 r_work: 0.3706 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 15726 Z= 0.299 Angle : 0.871 10.475 21508 Z= 0.461 Chirality : 0.053 0.294 2318 Planarity : 0.008 0.064 2602 Dihedral : 14.765 63.716 2434 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 6.46 % Allowed : 20.27 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.19), residues: 1757 helix: 0.45 (0.19), residues: 756 sheet: 0.23 (0.31), residues: 233 loop : -0.74 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 241 HIS 0.010 0.002 HIS C 258 PHE 0.024 0.003 PHE A 197 TYR 0.022 0.003 TYR A1108 ARG 0.010 0.001 ARG A 309 Details of bonding type rmsd hydrogen bonds : bond 0.08674 ( 718) hydrogen bonds : angle 5.10930 ( 1938) SS BOND : bond 0.01090 ( 1) SS BOND : angle 1.37324 ( 2) covalent geometry : bond 0.00681 (15725) covalent geometry : angle 0.87070 (21506) *********************** 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 424 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 324 time to evaluate : 1.692 Fit side-chains REVERT: A 152 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6337 (tm-30) REVERT: A 165 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7093 (ptpp) REVERT: A 361 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7324 (tmm160) REVERT: A 374 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7273 (ptm160) REVERT: A 456 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: A 994 TRP cc_start: 0.4495 (OUTLIER) cc_final: 0.2447 (m100) REVERT: A 1175 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.6610 (tm-30) REVERT: B 170 PHE cc_start: 0.6675 (OUTLIER) cc_final: 0.6081 (t80) REVERT: B 347 LEU cc_start: 0.8515 (tp) cc_final: 0.8271 (tm) REVERT: B 400 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: B 404 ASN cc_start: 0.8545 (m-40) cc_final: 0.8291 (m110) REVERT: C 219 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.6145 (t80) REVERT: C 236 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7001 (mp0) outliers start: 100 outliers final: 43 residues processed: 386 average time/residue: 1.1970 time to fit residues: 510.7097 Evaluate side-chains 371 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 317 time to evaluate : 1.700 ------------------------------------------------------------------------------- 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 152 GLU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 305 SER 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 464 MET Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 773 LYS 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 890 ASP 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 1063 SER 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 1201 SER Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 449 GLU 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 236 GLU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 407 LEU 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 112 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS A 968 GLN B 74 GLN B 258 HIS B 305 ASN C 74 GLN 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 = 0.136218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.128131 restraints weight = 25901.078| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.24 r_work: 0.3764 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15726 Z= 0.153 Angle : 0.700 11.672 21508 Z= 0.363 Chirality : 0.044 0.311 2318 Planarity : 0.005 0.059 2602 Dihedral : 14.473 60.426 2434 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.68 % Allowed : 23.37 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1757 helix: 0.84 (0.19), residues: 759 sheet: 0.64 (0.32), residues: 234 loop : -0.53 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 241 HIS 0.010 0.001 HIS C 309 PHE 0.018 0.002 PHE A 961 TYR 0.018 0.002 TYR A1108 ARG 0.009 0.001 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.05812 ( 718) hydrogen bonds : angle 4.74735 ( 1938) SS BOND : bond 0.00496 ( 1) SS BOND : angle 0.83001 ( 2) covalent geometry : bond 0.00332 (15725) covalent geometry : angle 0.70023 (21506) *********************** 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 394 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 337 time to evaluate : 1.610 Fit side-chains REVERT: A 152 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6390 (tm-30) REVERT: A 361 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7576 (ttm170) REVERT: A 456 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7566 (tt0) REVERT: A 658 LYS cc_start: 0.8034 (tmmt) cc_final: 0.7630 (ttpt) REVERT: A 994 TRP cc_start: 0.4082 (OUTLIER) cc_final: 0.2566 (t-100) REVERT: B 170 PHE cc_start: 0.6496 (OUTLIER) cc_final: 0.5786 (t80) REVERT: B 347 LEU cc_start: 0.8428 (tp) cc_final: 0.8220 (tm) REVERT: B 400 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: C 219 PHE cc_start: 0.6949 (OUTLIER) cc_final: 0.6071 (t80) REVERT: C 419 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6263 (tp30) REVERT: C 465 MET cc_start: 0.7119 (tpp) cc_final: 0.6763 (mpp) REVERT: C 479 ILE cc_start: 0.8189 (mm) cc_final: 0.7932 (tp) outliers start: 57 outliers final: 32 residues processed: 374 average time/residue: 1.2217 time to fit residues: 506.1306 Evaluate side-chains 363 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 323 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 361 ARG 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 593 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 773 LYS 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 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 1136 GLU Chi-restraints excluded: chain A residue 1141 VAL 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 170 PHE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 400 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 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 419 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 87 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN A 550 GLN ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 HIS B 74 GLN B 305 ASN C 74 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.134268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.126209 restraints weight = 25697.776| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.23 r_work: 0.3738 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15726 Z= 0.201 Angle : 0.760 10.617 21508 Z= 0.397 Chirality : 0.047 0.327 2318 Planarity : 0.006 0.061 2602 Dihedral : 14.596 61.992 2434 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.39 % Allowed : 23.05 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1757 helix: 0.66 (0.19), residues: 763 sheet: 0.38 (0.31), residues: 246 loop : -0.66 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 241 HIS 0.009 0.002 HIS C 309 PHE 0.018 0.002 PHE A 197 TYR 0.020 0.002 TYR A1108 ARG 0.010 0.001 ARG A 309 Details of bonding type rmsd hydrogen bonds : bond 0.06954 ( 718) hydrogen bonds : angle 4.89095 ( 1938) SS BOND : bond 0.00700 ( 1) SS BOND : angle 1.05462 ( 2) covalent geometry : bond 0.00453 (15725) covalent geometry : angle 0.76037 (21506) *********************** 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 395 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 327 time to evaluate : 1.922 Fit side-chains REVERT: A 152 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6395 (tm-30) REVERT: A 361 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7582 (ttm170) REVERT: A 374 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7247 (ptm160) REVERT: A 456 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: A 977 GLU cc_start: 0.6900 (mp0) cc_final: 0.6650 (mp0) REVERT: A 994 TRP cc_start: 0.4074 (OUTLIER) cc_final: 0.2437 (t-100) REVERT: A 1175 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: B 122 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.6908 (mpp-170) REVERT: B 170 PHE cc_start: 0.6539 (OUTLIER) cc_final: 0.5819 (t80) REVERT: B 347 LEU cc_start: 0.8471 (tp) cc_final: 0.8259 (tm) REVERT: B 389 ARG cc_start: 0.6161 (OUTLIER) cc_final: 0.5735 (ppt170) REVERT: B 400 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: C 219 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6098 (t80) outliers start: 68 outliers final: 37 residues processed: 373 average time/residue: 1.2006 time to fit residues: 494.9494 Evaluate side-chains 366 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 318 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 305 SER 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 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 773 LYS 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 1141 VAL 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 122 ARG Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 280 ASP 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 219 PHE Chi-restraints excluded: chain C residue 228 VAL 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 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 113 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 153 optimal weight: 0.1980 chunk 154 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 569 HIS B 74 GLN B 258 HIS B 305 ASN C 74 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.137485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.129394 restraints weight = 26280.613| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.26 r_work: 0.3783 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15726 Z= 0.140 Angle : 0.701 13.540 21508 Z= 0.359 Chirality : 0.044 0.350 2318 Planarity : 0.005 0.055 2602 Dihedral : 14.422 59.914 2434 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.97 % Allowed : 24.98 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1757 helix: 0.97 (0.19), residues: 754 sheet: 0.52 (0.31), residues: 247 loop : -0.42 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 241 HIS 0.011 0.001 HIS C 309 PHE 0.016 0.001 PHE A 961 TYR 0.014 0.001 TYR B 290 ARG 0.010 0.001 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.05279 ( 718) hydrogen bonds : angle 4.66422 ( 1938) SS BOND : bond 0.00402 ( 1) SS BOND : angle 0.72574 ( 2) covalent geometry : bond 0.00304 (15725) covalent geometry : angle 0.70091 (21506) ********************** 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 383 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 337 time to evaluate : 1.579 Fit side-chains REVERT: A 152 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6320 (tm-30) REVERT: A 361 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7579 (ttm170) REVERT: A 456 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: A 658 LYS cc_start: 0.7997 (tmmt) cc_final: 0.7564 (ttpt) REVERT: A 977 GLU cc_start: 0.6892 (mp0) cc_final: 0.6676 (mp0) REVERT: A 994 TRP cc_start: 0.3911 (OUTLIER) cc_final: 0.2294 (t-100) REVERT: B 170 PHE cc_start: 0.6533 (OUTLIER) cc_final: 0.5780 (t80) REVERT: B 219 PHE cc_start: 0.6367 (OUTLIER) cc_final: 0.5319 (p90) REVERT: B 400 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7294 (tm-30) REVERT: C 197 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.7998 (tt) REVERT: C 219 PHE cc_start: 0.6862 (OUTLIER) cc_final: 0.5907 (t80) REVERT: C 465 MET cc_start: 0.7020 (tpp) cc_final: 0.6610 (mpp) REVERT: C 479 ILE cc_start: 0.8188 (mm) cc_final: 0.7955 (tp) outliers start: 46 outliers final: 26 residues processed: 368 average time/residue: 1.1400 time to fit residues: 465.1112 Evaluate side-chains 361 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 326 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 361 ARG 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 593 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 773 LYS 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 994 TRP Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 280 ASP 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 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 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 8 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 HIS B 305 ASN C 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.135374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.127287 restraints weight = 25784.725| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.23 r_work: 0.3754 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15726 Z= 0.179 Angle : 0.749 13.514 21508 Z= 0.386 Chirality : 0.046 0.331 2318 Planarity : 0.006 0.056 2602 Dihedral : 14.500 60.911 2434 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.62 % Allowed : 24.60 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1757 helix: 0.83 (0.19), residues: 758 sheet: 0.46 (0.31), residues: 244 loop : -0.50 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 241 HIS 0.009 0.001 HIS C 309 PHE 0.017 0.002 PHE A 969 TYR 0.019 0.002 TYR A1108 ARG 0.010 0.001 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.06305 ( 718) hydrogen bonds : angle 4.79533 ( 1938) SS BOND : bond 0.00640 ( 1) SS BOND : angle 1.00118 ( 2) covalent geometry : bond 0.00401 (15725) covalent geometry : angle 0.74879 (21506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13750.95 seconds wall clock time: 236 minutes 24.95 seconds (14184.95 seconds total)