Starting phenix.real_space_refine on Sat Oct 11 14:23:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8udl_42150/10_2025/8udl_42150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8udl_42150/10_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_42150/10_2025/8udl_42150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8udl_42150/10_2025/8udl_42150.map" model { file = "/net/cci-nas-00/data/ceres_data/8udl_42150/10_2025/8udl_42150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8udl_42150/10_2025/8udl_42150.cif" } resolution = 2.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.366 sd= 0.630 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 46 5.49 5 S 82 5.16 5 C 9579 2.51 5 N 2679 2.21 5 O 2859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15245 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7778 Classifications: {'peptide': 974} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 65, 'TRANS': 908} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3300 Classifications: {'peptide': 410} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3222 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 2 Chain: "P" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "T" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 494 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Time building chain proxies: 3.42, per 1000 atoms: 0.22 Number of scatterers: 15245 At special positions: 0 Unit cell: (115.24, 109.22, 153.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 46 15.00 O 2859 8.00 N 2679 7.00 C 9579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A1077 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 597.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 14 sheets defined 49.9% alpha, 13.5% beta 20 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 72 through 76 removed outlier: 4.287A pdb=" N ILE A 76 " --> pdb=" O PRO A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 96 through 111 removed outlier: 3.564A pdb=" N HIS A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 158 Proline residue: A 149 - end of helix removed outlier: 3.535A pdb=" N LEU A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 270 through 276 removed outlier: 4.094A pdb=" N ASP A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 6.653A pdb=" N GLU A 280 " --> pdb=" O HIS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 305 through 315 removed outlier: 3.507A pdb=" N SER A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 removed outlier: 3.856A pdb=" N ASP A 349 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 351 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 removed outlier: 3.698A pdb=" N GLN A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.173A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 471 removed outlier: 3.815A pdb=" N ARG A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 482 removed outlier: 3.680A pdb=" N SER A 475 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY A 476 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 478 " --> pdb=" O SER A 475 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 554 Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 570 through 576 removed outlier: 3.736A pdb=" N LEU A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 650 through 663 Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 786 through 810 removed outlier: 5.117A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 858 through 862 removed outlier: 3.563A pdb=" N ALA A 862 " --> pdb=" O TRP A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 878 removed outlier: 4.385A pdb=" N LYS A 875 " --> pdb=" O SER A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 908 Processing helix chain 'A' and resid 914 through 923 Processing helix chain 'A' and resid 930 through 939 removed outlier: 3.544A pdb=" N VAL A 939 " --> pdb=" O THR A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 955 removed outlier: 3.727A pdb=" N ILE A 948 " --> pdb=" O GLU A 944 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 955 " --> pdb=" O TYR A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 974 through 990 Processing helix chain 'A' and resid 1054 through 1067 Processing helix chain 'A' and resid 1080 through 1084 Processing helix chain 'A' and resid 1092 through 1123 removed outlier: 3.798A pdb=" N VAL A1100 " --> pdb=" O ARG A1096 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1168 removed outlier: 3.535A pdb=" N ALA A1150 " --> pdb=" O ARG A1146 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A1151 " --> pdb=" O TYR A1147 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A1168 " --> pdb=" O PHE A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1178 Processing helix chain 'A' and resid 1205 through 1210 Processing helix chain 'A' and resid 1219 through 1228 Processing helix chain 'B' and resid 65 through 76 Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.706A pdb=" N ARG B 154 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU B 155 " --> pdb=" O THR B 152 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 156 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 168 removed outlier: 4.027A pdb=" N VAL B 168 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 177 removed outlier: 3.812A pdb=" N ASN B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 267 removed outlier: 4.024A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B 267 " --> pdb=" O TRP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 318 through 322 Processing helix chain 'B' and resid 342 through 354 removed outlier: 3.685A pdb=" N PHE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 391 through 409 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 444 through 451 removed outlier: 3.833A pdb=" N LEU B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 449 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 483 removed outlier: 3.941A pdb=" N LYS B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 150 through 157 removed outlier: 3.737A pdb=" N LEU C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.648A pdb=" N LEU C 162 " --> pdb=" O ASP C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 177 removed outlier: 4.327A pdb=" N LEU C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 172 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 191 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.409A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 318 through 322 removed outlier: 3.634A pdb=" N LYS C 321 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.600A pdb=" N PHE C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 409 removed outlier: 3.814A pdb=" N GLN C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 removed outlier: 3.882A pdb=" N THR C 420 " --> pdb=" O TYR C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.614A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 484 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 186 removed outlier: 3.530A pdb=" N SER A 222 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TRP A 220 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 195 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 435 through 438 removed outlier: 3.674A pdb=" N VAL A 814 " --> pdb=" O ALA A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 748 through 751 Processing sheet with id=AA4, first strand: chain 'A' and resid 1127 through 1132 removed outlier: 6.763A pdb=" N ARG A1138 " --> pdb=" O CYS A1130 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A1132 " --> pdb=" O GLU A1136 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU A1136 " --> pdb=" O SER A1132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 991 through 992 Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.372A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR B 206 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL B 335 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN B 305 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA8, first strand: chain 'B' and resid 145 through 146 Processing sheet with id=AA9, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AB1, first strand: chain 'B' and resid 413 through 414 removed outlier: 7.092A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 125 through 127 removed outlier: 3.504A pdb=" N TYR C 206 " --> pdb=" O PHE C 242 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER C 230 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL C 335 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE C 293 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS C 285 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 133 through 134 Processing sheet with id=AB4, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB5, first strand: chain 'C' and resid 413 through 415 removed outlier: 6.839A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 442 " --> pdb=" O HIS C 454 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS C 454 " --> pdb=" O LEU C 442 " (cutoff:3.500A) 667 hydrogen bonds defined for protein. 1836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 2.93 Time building geometry restraints manager: 1.65 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: 1.930 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.430 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.19), residues: 1757 helix: -0.82 (0.17), residues: 769 sheet: 0.89 (0.31), residues: 242 loop : -0.47 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.003 ARG B 259 TYR 0.022 0.004 TYR C 432 PHE 0.029 0.002 PHE A 197 TRP 0.024 0.003 TRP A 572 HIS 0.007 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00323 (15725) covalent geometry : angle 0.73641 (21506) SS BOND : bond 0.00814 ( 1) SS BOND : angle 0.92466 ( 2) hydrogen bonds : bond 0.17806 ( 718) hydrogen bonds : angle 6.20254 ( 1938) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 523 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 HIS cc_start: 0.6996 (m170) cc_final: 0.6743 (m170) REVERT: A 616 GLU cc_start: 0.7270 (tp30) cc_final: 0.6813 (tp30) REVERT: A 1066 THR cc_start: 0.7873 (m) cc_final: 0.7619 (p) REVERT: B 64 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6141 (mm-30) REVERT: B 170 PHE cc_start: 0.6582 (t80) cc_final: 0.6380 (t80) REVERT: C 219 PHE cc_start: 0.6663 (OUTLIER) cc_final: 0.5756 (t80) outliers start: 6 outliers final: 2 residues processed: 528 average time/residue: 0.6339 time to fit residues: 365.5969 Evaluate side-chains 380 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 376 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1184 ASP Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 228 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 468 ASN A 493 GLN A 565 HIS A 945 HIS A 968 GLN B 74 GLN B 305 ASN B 404 ASN C 74 GLN C 305 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.138112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.129771 restraints weight = 25669.169| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.25 r_work: 0.3784 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15726 Z= 0.181 Angle : 0.721 10.885 21508 Z= 0.389 Chirality : 0.046 0.228 2318 Planarity : 0.006 0.062 2602 Dihedral : 14.522 59.926 2440 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 4.78 % Allowed : 14.65 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.20), residues: 1757 helix: 0.46 (0.19), residues: 777 sheet: 1.07 (0.31), residues: 240 loop : -0.22 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 146 TYR 0.020 0.002 TYR A1108 PHE 0.024 0.002 PHE A 197 TRP 0.017 0.002 TRP B 241 HIS 0.008 0.001 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00383 (15725) covalent geometry : angle 0.72061 (21506) SS BOND : bond 0.00640 ( 1) SS BOND : angle 0.73359 ( 2) hydrogen bonds : bond 0.06823 ( 718) hydrogen bonds : angle 5.03999 ( 1938) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 372 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7333 (tmm160) REVERT: A 603 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7999 (mtt) REVERT: A 1175 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.6300 (tm-30) REVERT: B 219 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.5434 (p90) REVERT: B 464 GLU cc_start: 0.7163 (tp30) cc_final: 0.6871 (mm-30) REVERT: C 219 PHE cc_start: 0.6759 (OUTLIER) cc_final: 0.5920 (t80) REVERT: C 236 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7022 (mp0) outliers start: 74 outliers final: 25 residues processed: 411 average time/residue: 0.5942 time to fit residues: 268.3551 Evaluate side-chains 373 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 342 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 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 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 407 LEU Chi-restraints excluded: chain C residue 481 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 chunk 11 optimal weight: 0.0870 chunk 125 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN A 354 ASN A1110 HIS 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 = 0.3991 r_free = 0.3991 target = 0.139689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.131370 restraints weight = 26056.878| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.25 r_work: 0.3808 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15726 Z= 0.134 Angle : 0.620 7.172 21508 Z= 0.332 Chirality : 0.043 0.192 2318 Planarity : 0.005 0.055 2602 Dihedral : 14.264 59.962 2435 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.52 % Allowed : 16.01 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.20), residues: 1757 helix: 1.06 (0.19), residues: 760 sheet: 1.03 (0.31), residues: 250 loop : -0.12 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 443 TYR 0.017 0.001 TYR A1108 PHE 0.019 0.002 PHE A 961 TRP 0.016 0.001 TRP B 241 HIS 0.006 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00275 (15725) covalent geometry : angle 0.62025 (21506) SS BOND : bond 0.00468 ( 1) SS BOND : angle 0.69457 ( 2) hydrogen bonds : bond 0.05312 ( 718) hydrogen bonds : angle 4.60490 ( 1938) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 360 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7284 (tmm160) REVERT: A 860 LEU cc_start: 0.8602 (mm) cc_final: 0.8360 (tm) REVERT: A 994 TRP cc_start: 0.4302 (OUTLIER) cc_final: 0.2702 (t-100) REVERT: B 134 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7742 (mptt) REVERT: B 219 PHE cc_start: 0.6387 (OUTLIER) cc_final: 0.5338 (p90) REVERT: B 347 LEU cc_start: 0.8374 (tp) cc_final: 0.8146 (tm) REVERT: C 219 PHE cc_start: 0.6885 (OUTLIER) cc_final: 0.6016 (t80) REVERT: C 309 HIS cc_start: 0.6040 (p90) cc_final: 0.5831 (p-80) outliers start: 70 outliers final: 30 residues processed: 399 average time/residue: 0.5821 time to fit residues: 255.7556 Evaluate side-chains 372 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 337 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 299 MET 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 551 LYS 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 892 ASP 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 1136 GLU Chi-restraints excluded: chain A residue 1141 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 219 PHE Chi-restraints excluded: chain B residue 277 ASP 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 239 LEU Chi-restraints excluded: chain C residue 374 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 151 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 157 optimal weight: 0.0060 chunk 55 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 569 HIS B 74 GLN B 305 ASN B 404 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 = 0.3969 r_free = 0.3969 target = 0.137977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.129758 restraints weight = 26105.958| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.26 r_work: 0.3784 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15726 Z= 0.154 Angle : 0.647 7.810 21508 Z= 0.344 Chirality : 0.044 0.255 2318 Planarity : 0.005 0.058 2602 Dihedral : 14.275 59.697 2434 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.36 % Allowed : 17.04 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.20), residues: 1757 helix: 1.01 (0.19), residues: 763 sheet: 1.04 (0.31), residues: 241 loop : -0.21 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 443 TYR 0.018 0.002 TYR A1108 PHE 0.018 0.002 PHE A 197 TRP 0.020 0.002 TRP B 241 HIS 0.006 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00329 (15725) covalent geometry : angle 0.64648 (21506) SS BOND : bond 0.00563 ( 1) SS BOND : angle 0.85964 ( 2) hydrogen bonds : bond 0.05846 ( 718) hydrogen bonds : angle 4.61197 ( 1938) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 345 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 361 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7274 (tmm160) REVERT: A 456 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: A 478 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7071 (mtp85) REVERT: A 860 LEU cc_start: 0.8607 (mm) cc_final: 0.8363 (tm) REVERT: A 994 TRP cc_start: 0.3997 (OUTLIER) cc_final: 0.2596 (t-100) REVERT: A 1175 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.6578 (tm-30) REVERT: B 170 PHE cc_start: 0.6343 (OUTLIER) cc_final: 0.5905 (t80) REVERT: B 219 PHE cc_start: 0.6451 (OUTLIER) cc_final: 0.5400 (p90) REVERT: B 347 LEU cc_start: 0.8428 (tp) cc_final: 0.8209 (tm) REVERT: C 134 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7710 (mptt) REVERT: C 219 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.6030 (t80) REVERT: C 408 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6793 (tp30) outliers start: 83 outliers final: 34 residues processed: 391 average time/residue: 0.5892 time to fit residues: 253.4237 Evaluate side-chains 376 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 334 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 299 MET 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 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 586 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 892 ASP Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 948 ILE 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 1142 ARG Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 550 GLN A 569 HIS A 959 GLN B 74 GLN B 305 ASN C 74 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.140029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.131878 restraints weight = 25995.943| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.25 r_work: 0.3818 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15726 Z= 0.123 Angle : 0.596 11.325 21508 Z= 0.314 Chirality : 0.041 0.274 2318 Planarity : 0.005 0.048 2602 Dihedral : 14.184 59.740 2434 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.00 % Allowed : 18.53 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.20), residues: 1757 helix: 1.23 (0.19), residues: 761 sheet: 1.12 (0.31), residues: 246 loop : -0.19 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 443 TYR 0.016 0.001 TYR C 432 PHE 0.014 0.001 PHE A 197 TRP 0.026 0.001 TRP B 304 HIS 0.007 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00256 (15725) covalent geometry : angle 0.59641 (21506) SS BOND : bond 0.00359 ( 1) SS BOND : angle 0.64078 ( 2) hydrogen bonds : bond 0.04825 ( 718) hydrogen bonds : angle 4.43814 ( 1938) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 340 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 361 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7536 (ttm170) REVERT: A 456 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: A 478 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7038 (mtp85) REVERT: A 994 TRP cc_start: 0.4036 (OUTLIER) cc_final: 0.2306 (t-100) REVERT: A 1175 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6546 (tm-30) REVERT: B 170 PHE cc_start: 0.6420 (OUTLIER) cc_final: 0.5922 (t80) REVERT: B 219 PHE cc_start: 0.6426 (OUTLIER) cc_final: 0.5327 (p90) REVERT: B 347 LEU cc_start: 0.8369 (tp) cc_final: 0.8156 (tm) REVERT: C 134 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7674 (mptt) REVERT: C 219 PHE cc_start: 0.6973 (OUTLIER) cc_final: 0.6044 (t80) outliers start: 62 outliers final: 31 residues processed: 377 average time/residue: 0.5776 time to fit residues: 240.2124 Evaluate side-chains 370 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 331 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 305 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 478 ARG 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 892 ASP Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 902 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 1064 ILE 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 1201 SER Chi-restraints excluded: chain A residue 1226 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 9 optimal weight: 0.0050 chunk 141 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 167 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 overall best weight: 1.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 550 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.138718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.130534 restraints weight = 25902.071| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.25 r_work: 0.3799 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3318 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= 0.141 Angle : 0.630 10.269 21508 Z= 0.330 Chirality : 0.043 0.282 2318 Planarity : 0.005 0.054 2602 Dihedral : 14.199 59.710 2434 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.13 % Allowed : 19.50 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.20), residues: 1757 helix: 1.22 (0.19), residues: 762 sheet: 1.01 (0.31), residues: 252 loop : -0.21 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 443 TYR 0.020 0.002 TYR C 432 PHE 0.016 0.001 PHE A 197 TRP 0.026 0.001 TRP B 304 HIS 0.012 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00304 (15725) covalent geometry : angle 0.63011 (21506) SS BOND : bond 0.00482 ( 1) SS BOND : angle 0.81676 ( 2) hydrogen bonds : bond 0.05304 ( 718) hydrogen bonds : angle 4.47185 ( 1938) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 340 time to evaluate : 0.605 Fit side-chains REVERT: A 361 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7528 (ttm170) REVERT: A 456 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: A 994 TRP cc_start: 0.4138 (OUTLIER) cc_final: 0.2341 (t-100) REVERT: A 1175 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6609 (tm-30) REVERT: B 170 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.5963 (t80) REVERT: B 219 PHE cc_start: 0.6419 (OUTLIER) cc_final: 0.5287 (p90) REVERT: B 347 LEU cc_start: 0.8402 (tp) cc_final: 0.8179 (tm) REVERT: B 400 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7505 (mm-40) REVERT: C 219 PHE cc_start: 0.6969 (OUTLIER) cc_final: 0.5998 (t80) outliers start: 64 outliers final: 31 residues processed: 377 average time/residue: 0.5927 time to fit residues: 246.1098 Evaluate side-chains 364 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 325 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 305 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 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 892 ASP Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 948 ILE 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 1142 ARG Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 219 PHE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 22 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 134 optimal weight: 0.0000 chunk 65 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 157 optimal weight: 0.0060 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 305 ASN C 74 GLN C 323 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.135929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.127834 restraints weight = 25806.787| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.24 r_work: 0.3761 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15726 Z= 0.184 Angle : 0.709 11.145 21508 Z= 0.373 Chirality : 0.046 0.279 2318 Planarity : 0.006 0.055 2602 Dihedral : 14.378 60.477 2434 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.78 % Allowed : 19.56 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.20), residues: 1757 helix: 0.95 (0.19), residues: 764 sheet: 0.83 (0.31), residues: 235 loop : -0.37 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 443 TYR 0.023 0.002 TYR C 432 PHE 0.019 0.002 PHE C 170 TRP 0.020 0.002 TRP B 304 HIS 0.011 0.002 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00410 (15725) covalent geometry : angle 0.70866 (21506) SS BOND : bond 0.00673 ( 1) SS BOND : angle 1.00598 ( 2) hydrogen bonds : bond 0.06598 ( 718) hydrogen bonds : angle 4.72971 ( 1938) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 328 time to evaluate : 0.562 Fit side-chains REVERT: A 361 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7273 (tmm160) REVERT: A 456 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: A 478 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7116 (mtp85) REVERT: A 658 LYS cc_start: 0.8018 (tmmt) cc_final: 0.7624 (ttpt) REVERT: A 994 TRP cc_start: 0.4193 (OUTLIER) cc_final: 0.2362 (t-100) REVERT: A 1175 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.6681 (tm-30) REVERT: B 170 PHE cc_start: 0.6638 (OUTLIER) cc_final: 0.5957 (t80) REVERT: B 347 LEU cc_start: 0.8467 (tp) cc_final: 0.8259 (tm) REVERT: B 389 ARG cc_start: 0.6184 (OUTLIER) cc_final: 0.5734 (ppt170) REVERT: C 219 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6011 (t80) REVERT: C 236 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7081 (mt-10) outliers start: 74 outliers final: 36 residues processed: 373 average time/residue: 0.5726 time to fit residues: 236.0352 Evaluate side-chains 366 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 321 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 299 MET 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 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 456 GLN Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 586 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 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 93 SER Chi-restraints excluded: chain B residue 170 PHE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 389 ARG Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 107 optimal weight: 0.2980 chunk 111 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 140 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS A 959 GLN ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 305 ASN B 404 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 = 0.3970 r_free = 0.3970 target = 0.137971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.129870 restraints weight = 25949.283| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.25 r_work: 0.3791 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15726 Z= 0.143 Angle : 0.659 10.188 21508 Z= 0.343 Chirality : 0.043 0.302 2318 Planarity : 0.005 0.056 2602 Dihedral : 14.310 59.924 2434 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.07 % Allowed : 20.92 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.20), residues: 1757 helix: 1.10 (0.19), residues: 760 sheet: 0.85 (0.31), residues: 243 loop : -0.32 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 443 TYR 0.024 0.002 TYR C 432 PHE 0.017 0.001 PHE C 170 TRP 0.020 0.001 TRP B 241 HIS 0.011 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00308 (15725) covalent geometry : angle 0.65907 (21506) SS BOND : bond 0.00475 ( 1) SS BOND : angle 0.74986 ( 2) hydrogen bonds : bond 0.05408 ( 718) hydrogen bonds : angle 4.57216 ( 1938) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 335 time to evaluate : 0.636 Fit side-chains REVERT: A 361 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7243 (tmm160) REVERT: A 456 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: A 478 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7082 (mtp85) REVERT: A 994 TRP cc_start: 0.4122 (OUTLIER) cc_final: 0.2118 (m100) REVERT: A 1175 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6680 (tm-30) REVERT: B 170 PHE cc_start: 0.6526 (OUTLIER) cc_final: 0.5811 (t80) REVERT: B 219 PHE cc_start: 0.6446 (OUTLIER) cc_final: 0.5389 (p90) REVERT: B 389 ARG cc_start: 0.6206 (OUTLIER) cc_final: 0.5802 (ppt170) REVERT: C 219 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6021 (t80) REVERT: C 479 ILE cc_start: 0.8211 (mm) cc_final: 0.7934 (tp) outliers start: 63 outliers final: 35 residues processed: 370 average time/residue: 0.5840 time to fit residues: 238.1301 Evaluate side-chains 362 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 318 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 305 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 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 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 994 TRP Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1142 ARG Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 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 425 LEU 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 219 PHE Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 389 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 142 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 157 optimal weight: 0.0370 chunk 40 optimal weight: 0.0670 chunk 48 optimal weight: 3.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS A 618 HIS A 864 ASN A 968 GLN ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 305 ASN C 74 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.139291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.131120 restraints weight = 26076.274| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.25 r_work: 0.3806 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15726 Z= 0.129 Angle : 0.638 10.584 21508 Z= 0.330 Chirality : 0.043 0.339 2318 Planarity : 0.005 0.051 2602 Dihedral : 14.266 59.996 2434 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.36 % Allowed : 22.66 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.20), residues: 1757 helix: 1.20 (0.20), residues: 759 sheet: 0.85 (0.31), residues: 255 loop : -0.32 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 443 TYR 0.029 0.001 TYR C 432 PHE 0.020 0.001 PHE A 969 TRP 0.029 0.001 TRP B 241 HIS 0.012 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00277 (15725) covalent geometry : angle 0.63835 (21506) SS BOND : bond 0.00413 ( 1) SS BOND : angle 0.73865 ( 2) hydrogen bonds : bond 0.04978 ( 718) hydrogen bonds : angle 4.50019 ( 1938) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 334 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 361 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7564 (ttm170) REVERT: A 456 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7417 (mt0) REVERT: A 478 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7046 (mtp85) REVERT: A 658 LYS cc_start: 0.7973 (tmmt) cc_final: 0.7564 (ttpt) REVERT: A 927 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.6227 (mtt90) REVERT: A 994 TRP cc_start: 0.4136 (OUTLIER) cc_final: 0.2307 (t-100) REVERT: A 1175 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6712 (tm-30) REVERT: B 170 PHE cc_start: 0.6524 (OUTLIER) cc_final: 0.5768 (t80) REVERT: B 219 PHE cc_start: 0.6437 (OUTLIER) cc_final: 0.5363 (p90) REVERT: B 389 ARG cc_start: 0.6055 (OUTLIER) cc_final: 0.5664 (ppt170) REVERT: C 197 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7941 (tt) REVERT: C 219 PHE cc_start: 0.6974 (OUTLIER) cc_final: 0.5928 (t80) REVERT: C 479 ILE cc_start: 0.8136 (mm) cc_final: 0.7888 (tp) outliers start: 52 outliers final: 27 residues processed: 368 average time/residue: 0.5874 time to fit residues: 238.0225 Evaluate side-chains 352 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 314 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 305 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 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 892 ASP Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1142 ARG Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 62 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 569 HIS A 968 GLN ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 305 ASN B 404 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 = 0.3902 r_free = 0.3902 target = 0.132935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.124881 restraints weight = 26077.129| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.24 r_work: 0.3716 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 15726 Z= 0.287 Angle : 0.876 12.299 21508 Z= 0.462 Chirality : 0.053 0.322 2318 Planarity : 0.008 0.066 2602 Dihedral : 14.675 62.957 2434 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.68 % Allowed : 22.72 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.19), residues: 1757 helix: 0.48 (0.19), residues: 764 sheet: 0.32 (0.31), residues: 230 loop : -0.70 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1187 TYR 0.040 0.003 TYR C 432 PHE 0.024 0.003 PHE A 197 TRP 0.025 0.003 TRP B 304 HIS 0.009 0.002 HIS A 945 Details of bonding type rmsd covalent geometry : bond 0.00654 (15725) covalent geometry : angle 0.87586 (21506) SS BOND : bond 0.01069 ( 1) SS BOND : angle 1.36206 ( 2) hydrogen bonds : bond 0.08451 ( 718) hydrogen bonds : angle 5.09281 ( 1938) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 321 time to evaluate : 0.684 Fit side-chains REVERT: A 361 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7411 (tmm160) REVERT: A 456 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: A 994 TRP cc_start: 0.4523 (OUTLIER) cc_final: 0.2529 (t-100) REVERT: A 1175 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.6655 (tm-30) REVERT: B 170 PHE cc_start: 0.6677 (OUTLIER) cc_final: 0.5946 (t80) REVERT: B 389 ARG cc_start: 0.6083 (OUTLIER) cc_final: 0.5626 (ppt170) REVERT: C 219 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6121 (t80) REVERT: C 479 ILE cc_start: 0.8300 (mm) cc_final: 0.7962 (tp) outliers start: 57 outliers final: 32 residues processed: 358 average time/residue: 0.5791 time to fit residues: 228.5382 Evaluate side-chains 355 residues out of total 1553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 316 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 361 ARG Chi-restraints excluded: chain A residue 383 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 456 GLN 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 832 ASP 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 902 LEU Chi-restraints excluded: chain A residue 994 TRP Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1141 VAL Chi-restraints excluded: chain A residue 1175 GLN Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1201 SER Chi-restraints excluded: chain A residue 1226 LEU Chi-restraints excluded: chain B residue 93 SER 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 425 LEU 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 320 SER 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 21 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 40 optimal weight: 0.0370 chunk 59 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 170 optimal weight: 7.9990 chunk 180 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 chunk 70 optimal weight: 0.0020 overall best weight: 1.5268 ------------------------------------------------------------------------------- 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 ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3960 r_free = 0.3960 target = 0.137110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.129033 restraints weight = 25713.214| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.24 r_work: 0.3779 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3700 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= 0.150 Angle : 0.701 10.471 21508 Z= 0.363 Chirality : 0.044 0.324 2318 Planarity : 0.005 0.055 2602 Dihedral : 14.407 60.028 2434 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.65 % Allowed : 24.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.20), residues: 1757 helix: 0.90 (0.19), residues: 759 sheet: 0.51 (0.31), residues: 238 loop : -0.49 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 443 TYR 0.038 0.002 TYR C 432 PHE 0.017 0.002 PHE A 969 TRP 0.023 0.001 TRP B 241 HIS 0.012 0.001 HIS C 309 Details of bonding type rmsd covalent geometry : bond 0.00326 (15725) covalent geometry : angle 0.70107 (21506) SS BOND : bond 0.00482 ( 1) SS BOND : angle 0.75335 ( 2) hydrogen bonds : bond 0.05796 ( 718) hydrogen bonds : angle 4.73269 ( 1938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6849.14 seconds wall clock time: 116 minutes 56.73 seconds (7016.73 seconds total)