Starting phenix.real_space_refine on Fri Jul 3 14:17:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r95_53853/07_2026/9r95_53853.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r95_53853/07_2026/9r95_53853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r95_53853/07_2026/9r95_53853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r95_53853/07_2026/9r95_53853.map" model { file = "/net/cci-nas-00/data/ceres_data/9r95_53853/07_2026/9r95_53853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r95_53853/07_2026/9r95_53853.cif" } resolution = 3.2 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= 0.001 sd= 0.005 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 104 5.49 5 S 75 5.16 5 C 8900 2.51 5 N 2615 2.21 5 O 2826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14520 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8478 Classifications: {'peptide': 1066} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 68, 'TRANS': 997} Chain breaks: 3 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2572 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 21, 'TRANS': 304} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1362 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 166} Chain breaks: 2 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 5, 'PHE:plan': 2, 'TYR:plan': 3, 'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "R" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 77 Unusual residues: {'GTP': 1} Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="GTP R 1 " pdbres=" G R 2 " Chain: "N" Number of atoms: 1040 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 49, 1019 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Conformer: "B" Number of residues, atoms: 49, 1019 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} bond proxies already assigned to first conformer: 1122 Chain: "T" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 991 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A DA N 36 " occ=0.74 ... (40 atoms not shown) pdb=" C4 B DA N 36 " occ=0.26 Time building chain proxies: 3.48, per 1000 atoms: 0.24 Number of scatterers: 14520 At special positions: 0 Unit cell: (100.8, 129.6, 144, 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 75 16.00 P 104 15.00 O 2826 8.00 N 2615 7.00 C 8900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 596.8 milliseconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2994 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 11 sheets defined 62.9% alpha, 5.0% beta 43 base pairs and 76 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 122 through 146 removed outlier: 3.785A pdb=" N MET A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 181 Processing helix chain 'A' and resid 187 through 198 removed outlier: 4.167A pdb=" N ALA A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 237 removed outlier: 3.862A pdb=" N LEU A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 252 removed outlier: 3.968A pdb=" N ALA A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.663A pdb=" N LYS A 257 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.618A pdb=" N TYR A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 312 through 326 removed outlier: 4.092A pdb=" N ILE A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 removed outlier: 3.789A pdb=" N PHE A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 355 removed outlier: 4.148A pdb=" N VAL A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 410 removed outlier: 3.715A pdb=" N LEU A 396 " --> pdb=" O PRO A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 462 removed outlier: 3.692A pdb=" N ARG A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 473 Processing helix chain 'A' and resid 475 through 490 Processing helix chain 'A' and resid 497 through 521 removed outlier: 3.946A pdb=" N THR A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 534 removed outlier: 4.186A pdb=" N ALA A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 537 No H-bonds generated for 'chain 'A' and resid 535 through 537' Processing helix chain 'A' and resid 548 through 556 Processing helix chain 'A' and resid 568 through 587 removed outlier: 3.717A pdb=" N THR A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 635 removed outlier: 3.564A pdb=" N ALA A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 646 No H-bonds generated for 'chain 'A' and resid 644 through 646' Processing helix chain 'A' and resid 678 through 687 removed outlier: 3.552A pdb=" N CYS A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 691 Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 711 through 724 removed outlier: 3.623A pdb=" N ALA A 723 " --> pdb=" O GLN A 719 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 789 removed outlier: 4.281A pdb=" N GLU A 761 " --> pdb=" O GLU A 757 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 770 " --> pdb=" O GLN A 766 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU A 771 " --> pdb=" O LYS A 767 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 772 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 781 " --> pdb=" O ALA A 777 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 823 Processing helix chain 'A' and resid 837 through 850 Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 867 through 877 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 890 through 907 removed outlier: 3.559A pdb=" N LEU A 895 " --> pdb=" O PRO A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 936 Processing helix chain 'A' and resid 937 through 943 removed outlier: 3.660A pdb=" N SER A 943 " --> pdb=" O VAL A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 974 Processing helix chain 'A' and resid 975 through 981 removed outlier: 3.762A pdb=" N LEU A 981 " --> pdb=" O VAL A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 removed outlier: 3.828A pdb=" N VAL A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLN A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N THR A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1000 No H-bonds generated for 'chain 'A' and resid 998 through 1000' Processing helix chain 'A' and resid 1004 through 1017 removed outlier: 3.817A pdb=" N LEU A1008 " --> pdb=" O TYR A1004 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A1009 " --> pdb=" O GLY A1005 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A1012 " --> pdb=" O LEU A1008 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A1013 " --> pdb=" O GLN A1009 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1044 removed outlier: 3.569A pdb=" N GLU A1042 " --> pdb=" O LYS A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1064 Processing helix chain 'A' and resid 1111 through 1116 Processing helix chain 'A' and resid 1118 through 1141 removed outlier: 3.647A pdb=" N ASN A1122 " --> pdb=" O GLY A1118 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A1124 " --> pdb=" O PRO A1120 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A1141 " --> pdb=" O LEU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1177 removed outlier: 4.025A pdb=" N GLU A1177 " --> pdb=" O ARG A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1191 Processing helix chain 'A' and resid 1198 through 1209 Processing helix chain 'A' and resid 1218 through 1225 removed outlier: 3.716A pdb=" N GLN A1221 " --> pdb=" O ASP A1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 90 Processing helix chain 'B' and resid 107 through 117 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 168 through 177 removed outlier: 3.889A pdb=" N PHE B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 213 removed outlier: 3.709A pdb=" N SER B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 221 removed outlier: 3.542A pdb=" N PHE B 220 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.636A pdb=" N VAL B 252 " --> pdb=" O HIS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 271 Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 316 through 328 removed outlier: 4.129A pdb=" N PHE B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.872A pdb=" N HIS B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.531A pdb=" N ASN B 364 " --> pdb=" O LYS B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 380 removed outlier: 3.628A pdb=" N LYS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B 380 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 removed outlier: 3.553A pdb=" N GLU B 394 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 49 Processing helix chain 'C' and resid 55 through 72 Proline residue: C 66 - end of helix Processing helix chain 'C' and resid 76 through 91 Processing helix chain 'C' and resid 92 through 121 removed outlier: 3.549A pdb=" N LYS C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 151 Processing helix chain 'C' and resid 160 through 170 Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'C' and resid 199 through 226 removed outlier: 3.784A pdb=" N LYS C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN C 213 " --> pdb=" O THR C 209 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET C 222 " --> pdb=" O TRP C 218 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 415 Processing sheet with id=AA2, first strand: chain 'A' and resid 495 through 496 Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA4, first strand: chain 'A' and resid 707 through 709 Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 800 Processing sheet with id=AA6, first strand: chain 'A' and resid 831 through 832 removed outlier: 3.521A pdb=" N ARG A 831 " --> pdb=" O SER A 915 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 919 through 921 removed outlier: 3.567A pdb=" N TYR A1153 " --> pdb=" O GLN A 921 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1069 through 1071 Processing sheet with id=AA9, first strand: chain 'A' and resid 1089 through 1091 removed outlier: 4.074A pdb=" N LYS A1089 " --> pdb=" O TYR A1100 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A1098 " --> pdb=" O ILE A1091 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 74 removed outlier: 3.529A pdb=" N LYS B 72 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR B 74 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 148 removed outlier: 8.335A pdb=" N ILE B 147 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ALA B 122 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU B 99 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU B 123 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU B 101 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N MET B 194 " --> pdb=" O CYS B 102 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 191 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N PHE B 228 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLY B 193 " --> pdb=" O PHE B 228 " (cutoff:3.500A) 681 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 1.73 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: 4110 1.34 - 1.46: 2874 1.46 - 1.58: 7751 1.58 - 1.70: 205 1.70 - 1.82: 117 Bond restraints: 15057 Sorted by residual: bond pdb=" C3' DC T 12 " pdb=" C2' DC T 12 " ideal model delta sigma weight residual 1.516 1.566 -0.050 8.00e-03 1.56e+04 3.90e+01 bond pdb=" C4' DA T 45 " pdb=" O4' DA T 45 " ideal model delta sigma weight residual 1.446 1.503 -0.057 1.00e-02 1.00e+04 3.24e+01 bond pdb=" C LYS B 163 " pdb=" N PRO B 164 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.18e-02 7.18e+03 2.39e+01 bond pdb=" C4' DC T 42 " pdb=" O4' DC T 42 " ideal model delta sigma weight residual 1.446 1.481 -0.035 1.00e-02 1.00e+04 1.19e+01 bond pdb=" C3' DC T 25 " pdb=" C2' DC T 25 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.95e+00 ... (remaining 15052 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 20693 2.98 - 5.97: 114 5.97 - 8.95: 20 8.95 - 11.94: 8 11.94 - 14.92: 1 Bond angle restraints: 20836 Sorted by residual: angle pdb=" O4' DA T 45 " pdb=" C4' DA T 45 " pdb=" C3' DA T 45 " ideal model delta sigma weight residual 106.00 103.00 3.00 6.00e-01 2.78e+00 2.49e+01 angle pdb=" PB GTP R 1 " pdb=" O3B GTP R 1 " pdb=" PG GTP R 1 " ideal model delta sigma weight residual 120.50 135.42 -14.92 3.00e+00 1.11e-01 2.47e+01 angle pdb=" C3' DA N 39 " pdb=" O3' DA N 39 " pdb=" P DA N 40 " ideal model delta sigma weight residual 120.20 112.99 7.21 1.50e+00 4.44e-01 2.31e+01 angle pdb=" CB LYS B 295 " pdb=" CG LYS B 295 " pdb=" CD LYS B 295 " ideal model delta sigma weight residual 111.30 122.01 -10.71 2.30e+00 1.89e-01 2.17e+01 angle pdb=" C4' DA T 45 " pdb=" O4' DA T 45 " pdb=" C1' DA T 45 " ideal model delta sigma weight residual 110.10 105.67 4.43 1.00e+00 1.00e+00 1.96e+01 ... (remaining 20831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.28: 8283 34.28 - 68.56: 653 68.56 - 102.84: 22 102.84 - 137.13: 0 137.13 - 171.41: 3 Dihedral angle restraints: 8961 sinusoidal: 4365 harmonic: 4596 Sorted by residual: dihedral pdb=" C8 GTP R 1 " pdb=" C1' GTP R 1 " pdb=" N9 GTP R 1 " pdb=" O4' GTP R 1 " ideal model delta sinusoidal sigma weight residual 104.59 13.08 91.52 1 2.00e+01 2.50e-03 2.46e+01 dihedral pdb=" O3B GTP R 1 " pdb=" O3A GTP R 1 " pdb=" PB GTP R 1 " pdb=" PA GTP R 1 " ideal model delta sinusoidal sigma weight residual -68.92 -155.29 86.37 1 2.00e+01 2.50e-03 2.25e+01 dihedral pdb=" C4' DC T 36 " pdb=" C3' DC T 36 " pdb=" O3' DC T 36 " pdb=" P DA T 37 " ideal model delta sinusoidal sigma weight residual -140.00 31.41 -171.41 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2269 0.109 - 0.218: 42 0.218 - 0.327: 2 0.327 - 0.435: 3 0.435 - 0.544: 3 Chirality restraints: 2319 Sorted by residual: chirality pdb=" P DA N 39 " pdb=" OP1 DA N 39 " pdb=" OP2 DA N 39 " pdb=" O5' DA N 39 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.54 2.00e-01 2.50e+01 7.40e+00 chirality pdb=" P DC N 38 " pdb=" OP1 DC N 38 " pdb=" OP2 DC N 38 " pdb=" O5' DC N 38 " both_signs ideal model delta sigma weight residual True 2.34 -2.85 -0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" P DG T 15 " pdb=" OP1 DG T 15 " pdb=" OP2 DG T 15 " pdb=" O5' DG T 15 " both_signs ideal model delta sigma weight residual True 2.34 -2.85 -0.51 2.00e-01 2.50e+01 6.55e+00 ... (remaining 2316 not shown) Planarity restraints: 2319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 185 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO A 186 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 186 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 186 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA N 39 " -0.020 2.00e-02 2.50e+03 9.84e-03 2.66e+00 pdb=" N9 DA N 39 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA N 39 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA N 39 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA N 39 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA N 39 " -0.006 2.00e-02 2.50e+03 pdb=" N6 DA N 39 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DA N 39 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA N 39 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA N 39 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA N 39 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1101 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" C THR A1101 " -0.027 2.00e-02 2.50e+03 pdb=" O THR A1101 " 0.010 2.00e-02 2.50e+03 pdb=" N HIS A1102 " 0.009 2.00e-02 2.50e+03 ... (remaining 2316 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 286 2.68 - 3.23: 12776 3.23 - 3.79: 22616 3.79 - 4.34: 29153 4.34 - 4.90: 47508 Nonbonded interactions: 112339 Sorted by model distance: nonbonded pdb=" OH TYR A 530 " pdb=" O PRO A 651 " model vdw 2.121 3.040 nonbonded pdb=" OH TYR A1082 " pdb=" OP1 DC T 11 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR A 378 " pdb=" OD2 ASP A 697 " model vdw 2.210 3.040 nonbonded pdb=" O ALA A 182 " pdb=" OG SER A 185 " model vdw 2.274 3.040 nonbonded pdb=" O SER B 332 " pdb=" OG SER B 332 " model vdw 2.289 3.040 ... (remaining 112334 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.26 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.500 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15058 Z= 0.329 Angle : 0.692 14.924 20836 Z= 0.452 Chirality : 0.049 0.544 2319 Planarity : 0.004 0.046 2319 Dihedral : 20.502 171.408 5967 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.09 % Favored : 96.84 % Rotamer: Outliers : 1.51 % Allowed : 17.04 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.22), residues: 1552 helix: 1.87 (0.18), residues: 901 sheet: -0.28 (0.57), residues: 82 loop : -0.41 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 82 TYR 0.018 0.001 TYR A1100 PHE 0.016 0.001 PHE A 802 TRP 0.008 0.001 TRP A1026 HIS 0.005 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.33 (15057) covalent geometry : angle 0.69236 / 0.45 (20836) hydrogen bonds : bond 0.15582 / 10.20 ( 784) hydrogen bonds : angle 5.16533 / 3.72 ( 2180) Misc. bond : bond 0.04651 / 2.45 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 533 TYR cc_start: 0.9428 (OUTLIER) cc_final: 0.8393 (t80) REVERT: A 757 GLU cc_start: 0.5012 (pm20) cc_final: 0.4480 (mm-30) REVERT: A 772 MET cc_start: 0.7092 (tmm) cc_final: 0.6460 (ttp) REVERT: B 97 HIS cc_start: 0.6180 (OUTLIER) cc_final: 0.5087 (m90) REVERT: B 163 LYS cc_start: 0.8024 (mmtt) cc_final: 0.7698 (ttpt) REVERT: B 220 PHE cc_start: 0.8531 (m-80) cc_final: 0.8076 (m-10) REVERT: B 316 ASN cc_start: 0.8625 (t0) cc_final: 0.8169 (t0) REVERT: C 127 MET cc_start: 0.7665 (mmm) cc_final: 0.7225 (mpp) REVERT: C 169 ARG cc_start: 0.2887 (ttt-90) cc_final: 0.0465 (mtm180) REVERT: C 215 MET cc_start: 0.6186 (ptp) cc_final: 0.5955 (ptp) outliers start: 20 outliers final: 14 residues processed: 156 average time/residue: 0.1218 time to fit residues: 27.3992 Evaluate side-chains 146 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain C residue 222 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 40.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1009 GLN A1063 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.140433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.097287 restraints weight = 27128.030| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.24 r_work: 0.2994 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15058 Z= 0.155 Angle : 0.568 8.919 20836 Z= 0.312 Chirality : 0.040 0.322 2319 Planarity : 0.005 0.043 2319 Dihedral : 21.521 165.514 2891 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.11 % Allowed : 16.82 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.22), residues: 1552 helix: 1.97 (0.17), residues: 927 sheet: 0.33 (0.64), residues: 72 loop : -0.41 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 82 TYR 0.021 0.001 TYR C 103 PHE 0.015 0.001 PHE A 802 TRP 0.012 0.001 TRP C 88 HIS 0.007 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (15057) covalent geometry : angle 0.56843 / 0.31 (20836) hydrogen bonds : bond 0.05578 / 3.74 ( 784) hydrogen bonds : angle 3.84996 / 2.75 ( 2180) Misc. bond : bond 0.00548 / 0.29 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 533 TYR cc_start: 0.9525 (OUTLIER) cc_final: 0.8669 (t80) REVERT: A 757 GLU cc_start: 0.5579 (pm20) cc_final: 0.4919 (mm-30) REVERT: A 772 MET cc_start: 0.7293 (tmm) cc_final: 0.6827 (mtp) REVERT: B 97 HIS cc_start: 0.6407 (OUTLIER) cc_final: 0.5425 (m90) REVERT: B 163 LYS cc_start: 0.7932 (mmtt) cc_final: 0.7457 (mtpt) REVERT: B 220 PHE cc_start: 0.8460 (m-80) cc_final: 0.8159 (m-10) REVERT: B 316 ASN cc_start: 0.8509 (t0) cc_final: 0.8043 (t0) REVERT: C 80 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7296 (mt) REVERT: C 88 TRP cc_start: 0.7528 (t-100) cc_final: 0.7257 (t-100) REVERT: C 169 ARG cc_start: 0.1676 (ttt-90) cc_final: -0.0394 (mtm180) outliers start: 28 outliers final: 13 residues processed: 159 average time/residue: 0.1209 time to fit residues: 27.7466 Evaluate side-chains 149 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 80 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 73 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 0.0270 chunk 124 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 overall best weight: 2.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN A 304 GLN A 325 GLN C 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.141079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.097796 restraints weight = 26007.942| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.16 r_work: 0.3021 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15058 Z= 0.149 Angle : 0.548 8.750 20836 Z= 0.296 Chirality : 0.039 0.298 2319 Planarity : 0.005 0.045 2319 Dihedral : 21.462 166.239 2875 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.94 % Allowed : 16.97 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.22), residues: 1552 helix: 2.03 (0.17), residues: 927 sheet: 0.52 (0.65), residues: 72 loop : -0.43 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 82 TYR 0.020 0.001 TYR C 103 PHE 0.015 0.001 PHE A 802 TRP 0.012 0.001 TRP C 218 HIS 0.007 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (15057) covalent geometry : angle 0.54757 / 0.30 (20836) hydrogen bonds : bond 0.05091 / 3.41 ( 784) hydrogen bonds : angle 3.63704 / 2.59 ( 2180) Misc. bond : bond 0.00235 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 533 TYR cc_start: 0.9533 (OUTLIER) cc_final: 0.8671 (t80) REVERT: A 757 GLU cc_start: 0.5581 (pm20) cc_final: 0.4917 (mm-30) REVERT: A 772 MET cc_start: 0.7386 (tmm) cc_final: 0.6917 (mtp) REVERT: B 97 HIS cc_start: 0.6672 (OUTLIER) cc_final: 0.5705 (m90) REVERT: B 163 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7628 (ttpt) REVERT: B 220 PHE cc_start: 0.8544 (m-80) cc_final: 0.8188 (m-10) REVERT: B 316 ASN cc_start: 0.8613 (t0) cc_final: 0.8108 (t0) REVERT: C 127 MET cc_start: 0.7596 (mmm) cc_final: 0.7194 (mpp) REVERT: C 169 ARG cc_start: 0.2096 (ttt-90) cc_final: -0.0374 (mtm180) REVERT: C 210 ARG cc_start: 0.8366 (tmm160) cc_final: 0.8021 (ttp80) outliers start: 39 outliers final: 27 residues processed: 167 average time/residue: 0.1122 time to fit residues: 27.4804 Evaluate side-chains 157 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 965 VAL Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 17 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 148 optimal weight: 30.0000 chunk 155 optimal weight: 50.0000 chunk 157 optimal weight: 50.0000 chunk 154 optimal weight: 20.0000 chunk 68 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN A 325 GLN ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.138603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095547 restraints weight = 23208.356| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.08 r_work: 0.2970 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15058 Z= 0.210 Angle : 0.592 9.067 20836 Z= 0.317 Chirality : 0.041 0.300 2319 Planarity : 0.005 0.046 2319 Dihedral : 21.501 165.742 2875 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.47 % Allowed : 17.57 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.22), residues: 1552 helix: 1.93 (0.17), residues: 915 sheet: 0.22 (0.64), residues: 77 loop : -0.52 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 82 TYR 0.027 0.002 TYR C 103 PHE 0.020 0.001 PHE A 802 TRP 0.012 0.001 TRP C 88 HIS 0.008 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (15057) covalent geometry : angle 0.59164 / 0.32 (20836) hydrogen bonds : bond 0.05636 / 3.79 ( 784) hydrogen bonds : angle 3.72057 / 2.65 ( 2180) Misc. bond : bond 0.00052 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 533 TYR cc_start: 0.9541 (OUTLIER) cc_final: 0.8597 (t80) REVERT: A 757 GLU cc_start: 0.5529 (pm20) cc_final: 0.4923 (mm-30) REVERT: A 772 MET cc_start: 0.7369 (tmm) cc_final: 0.6871 (mtp) REVERT: A 1043 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8191 (ttt) REVERT: B 97 HIS cc_start: 0.6682 (OUTLIER) cc_final: 0.5707 (m90) REVERT: B 163 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7602 (ttpt) REVERT: B 220 PHE cc_start: 0.8592 (m-80) cc_final: 0.8250 (m-10) REVERT: C 55 SER cc_start: 0.8428 (t) cc_final: 0.7663 (p) REVERT: C 169 ARG cc_start: 0.2035 (ttt-90) cc_final: -0.0384 (mtm180) outliers start: 46 outliers final: 29 residues processed: 172 average time/residue: 0.1163 time to fit residues: 29.1872 Evaluate side-chains 158 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 965 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.140087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.096521 restraints weight = 27258.746| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.31 r_work: 0.2977 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15058 Z= 0.164 Angle : 0.564 9.051 20836 Z= 0.303 Chirality : 0.039 0.307 2319 Planarity : 0.005 0.046 2319 Dihedral : 21.464 165.206 2875 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.02 % Allowed : 18.25 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.22), residues: 1552 helix: 2.00 (0.17), residues: 915 sheet: 0.22 (0.63), residues: 77 loop : -0.52 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.021 0.001 TYR C 103 PHE 0.016 0.001 PHE A 802 TRP 0.013 0.001 TRP C 218 HIS 0.007 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (15057) covalent geometry : angle 0.56391 / 0.30 (20836) hydrogen bonds : bond 0.05152 / 3.46 ( 784) hydrogen bonds : angle 3.62228 / 2.58 ( 2180) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.6297 (mmp-170) cc_final: 0.6039 (mmp-170) REVERT: A 533 TYR cc_start: 0.9504 (OUTLIER) cc_final: 0.8661 (t80) REVERT: A 757 GLU cc_start: 0.5506 (pm20) cc_final: 0.4898 (mm-30) REVERT: A 772 MET cc_start: 0.7327 (tmm) cc_final: 0.6871 (mtp) REVERT: B 97 HIS cc_start: 0.6616 (OUTLIER) cc_final: 0.5665 (m90) REVERT: B 163 LYS cc_start: 0.8029 (mmtt) cc_final: 0.7596 (ttpt) REVERT: B 220 PHE cc_start: 0.8471 (m-80) cc_final: 0.8097 (m-10) REVERT: C 55 SER cc_start: 0.8287 (t) cc_final: 0.7674 (p) REVERT: C 127 MET cc_start: 0.7540 (mmm) cc_final: 0.7187 (mpp) REVERT: C 169 ARG cc_start: 0.1821 (ttt-90) cc_final: -0.0393 (mtm180) outliers start: 40 outliers final: 33 residues processed: 166 average time/residue: 0.1043 time to fit residues: 25.5011 Evaluate side-chains 162 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 965 VAL Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 1064 MET Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 78 optimal weight: 4.9990 chunk 52 optimal weight: 0.0470 chunk 76 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 108 optimal weight: 0.0060 chunk 85 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 65 optimal weight: 0.0670 overall best weight: 1.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN A 325 GLN C 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.142297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099628 restraints weight = 24760.912| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.11 r_work: 0.3030 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (15 function evaluations) r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15058 Z= 0.117 Angle : 0.526 8.956 20836 Z= 0.284 Chirality : 0.037 0.310 2319 Planarity : 0.004 0.046 2319 Dihedral : 21.360 163.769 2875 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.58 % Favored : 97.36 % Rotamer: Outliers : 2.56 % Allowed : 19.00 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.22), residues: 1552 helix: 2.14 (0.17), residues: 928 sheet: 0.16 (0.63), residues: 77 loop : -0.41 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 157 TYR 0.013 0.001 TYR C 103 PHE 0.011 0.001 PHE A 229 TRP 0.014 0.001 TRP C 218 HIS 0.005 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.12 (15057) covalent geometry : angle 0.52621 / 0.28 (20836) hydrogen bonds : bond 0.04143 / 2.76 ( 784) hydrogen bonds : angle 3.40292 / 2.43 ( 2180) Misc. bond : bond 0.00055 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.6290 (mmp-170) cc_final: 0.5540 (mmp-170) REVERT: A 461 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.8197 (t80) REVERT: A 757 GLU cc_start: 0.5466 (pm20) cc_final: 0.4870 (mm-30) REVERT: A 772 MET cc_start: 0.7282 (tmm) cc_final: 0.6801 (mtp) REVERT: B 97 HIS cc_start: 0.6711 (OUTLIER) cc_final: 0.5804 (m90) REVERT: B 163 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7571 (ttpt) REVERT: B 220 PHE cc_start: 0.8484 (m-80) cc_final: 0.8120 (m-10) REVERT: C 169 ARG cc_start: 0.1957 (ttt-90) cc_final: -0.0448 (mtm180) outliers start: 34 outliers final: 23 residues processed: 168 average time/residue: 0.1174 time to fit residues: 29.2016 Evaluate side-chains 154 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 120 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN A 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.142171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.098516 restraints weight = 33244.022| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.60 r_work: 0.3001 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15058 Z= 0.132 Angle : 0.543 10.402 20836 Z= 0.289 Chirality : 0.038 0.303 2319 Planarity : 0.004 0.046 2319 Dihedral : 21.344 164.141 2873 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.64 % Allowed : 19.08 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.22), residues: 1552 helix: 2.15 (0.17), residues: 928 sheet: 0.15 (0.62), residues: 77 loop : -0.45 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.013 0.001 TYR B 74 PHE 0.015 0.001 PHE A 802 TRP 0.014 0.001 TRP C 218 HIS 0.006 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (15057) covalent geometry : angle 0.54331 / 0.29 (20836) hydrogen bonds : bond 0.04330 / 2.89 ( 784) hydrogen bonds : angle 3.39549 / 2.43 ( 2180) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 158 ARG cc_start: 0.6344 (mmp-170) cc_final: 0.5575 (mmp-170) REVERT: A 461 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.8046 (t80) REVERT: A 757 GLU cc_start: 0.5519 (pm20) cc_final: 0.4934 (mm-30) REVERT: A 772 MET cc_start: 0.7261 (tmm) cc_final: 0.6793 (mtp) REVERT: B 97 HIS cc_start: 0.6699 (OUTLIER) cc_final: 0.5682 (m90) REVERT: B 163 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7564 (ttpt) REVERT: B 220 PHE cc_start: 0.8408 (m-80) cc_final: 0.8055 (m-10) REVERT: C 55 SER cc_start: 0.8242 (t) cc_final: 0.7594 (p) REVERT: C 127 MET cc_start: 0.7622 (mmm) cc_final: 0.7300 (mpp) REVERT: C 134 MET cc_start: 0.7854 (tpp) cc_final: 0.7644 (tpp) outliers start: 35 outliers final: 26 residues processed: 163 average time/residue: 0.1351 time to fit residues: 32.2840 Evaluate side-chains 160 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1063 HIS Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 21 optimal weight: 0.0670 chunk 90 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097802 restraints weight = 24394.714| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.09 r_work: 0.3021 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15058 Z= 0.151 Angle : 0.555 8.650 20836 Z= 0.295 Chirality : 0.039 0.306 2319 Planarity : 0.005 0.048 2319 Dihedral : 21.339 165.138 2873 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.49 % Allowed : 19.38 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.22), residues: 1552 helix: 2.12 (0.17), residues: 927 sheet: 0.14 (0.63), residues: 77 loop : -0.51 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.011 0.001 TYR C 103 PHE 0.016 0.001 PHE A 802 TRP 0.015 0.001 TRP C 218 HIS 0.006 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (15057) covalent geometry : angle 0.55476 / 0.29 (20836) hydrogen bonds : bond 0.04604 / 3.09 ( 784) hydrogen bonds : angle 3.44279 / 2.46 ( 2180) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.6372 (mmp-170) cc_final: 0.5661 (mmp-170) REVERT: A 461 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8217 (t80) REVERT: A 533 TYR cc_start: 0.9519 (OUTLIER) cc_final: 0.8660 (t80) REVERT: A 757 GLU cc_start: 0.5559 (pm20) cc_final: 0.4936 (mm-30) REVERT: A 772 MET cc_start: 0.7331 (tmm) cc_final: 0.6821 (mtp) REVERT: B 97 HIS cc_start: 0.6820 (OUTLIER) cc_final: 0.5749 (m90) REVERT: B 163 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7539 (mtpt) REVERT: B 220 PHE cc_start: 0.8508 (m-80) cc_final: 0.8139 (m-10) REVERT: C 55 SER cc_start: 0.8238 (t) cc_final: 0.7782 (p) REVERT: C 57 TYR cc_start: 0.6782 (t80) cc_final: 0.6306 (t80) REVERT: C 127 MET cc_start: 0.7636 (mmm) cc_final: 0.7297 (mpp) outliers start: 33 outliers final: 26 residues processed: 159 average time/residue: 0.1203 time to fit residues: 28.1534 Evaluate side-chains 161 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 130 optimal weight: 0.0470 chunk 150 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN A 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.141372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097981 restraints weight = 31534.652| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.53 r_work: 0.2992 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15058 Z= 0.132 Angle : 0.551 11.606 20836 Z= 0.291 Chirality : 0.038 0.309 2319 Planarity : 0.004 0.046 2319 Dihedral : 21.311 165.570 2873 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.34 % Allowed : 19.68 % Favored : 77.98 % 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 are not related in a simple way. whole: 1.74 (0.22), residues: 1552 helix: 2.16 (0.17), residues: 928 sheet: 0.34 (0.65), residues: 72 loop : -0.47 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 136 TYR 0.009 0.001 TYR C 103 PHE 0.014 0.001 PHE A 802 TRP 0.011 0.001 TRP C 218 HIS 0.006 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (15057) covalent geometry : angle 0.55087 / 0.29 (20836) hydrogen bonds : bond 0.04394 / 2.93 ( 784) hydrogen bonds : angle 3.40779 / 2.43 ( 2180) Misc. bond : bond 0.00027 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 158 ARG cc_start: 0.6239 (mmp-170) cc_final: 0.5449 (mmp-170) REVERT: A 461 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.8035 (t80) REVERT: A 757 GLU cc_start: 0.5529 (pm20) cc_final: 0.5018 (mm-30) REVERT: A 772 MET cc_start: 0.7236 (tmm) cc_final: 0.6757 (mtp) REVERT: B 97 HIS cc_start: 0.6661 (OUTLIER) cc_final: 0.5592 (m90) REVERT: B 163 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7457 (mtpt) REVERT: B 220 PHE cc_start: 0.8427 (m-80) cc_final: 0.8005 (m-10) REVERT: C 55 SER cc_start: 0.8240 (t) cc_final: 0.7738 (p) REVERT: C 57 TYR cc_start: 0.6625 (t80) cc_final: 0.6198 (t80) REVERT: C 127 MET cc_start: 0.7627 (mmm) cc_final: 0.7268 (mpp) REVERT: C 210 ARG cc_start: 0.8433 (ttp-170) cc_final: 0.8158 (ttp80) outliers start: 31 outliers final: 28 residues processed: 159 average time/residue: 0.1331 time to fit residues: 30.8981 Evaluate side-chains 160 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1002 THR Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 127 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 45 optimal weight: 0.0870 chunk 68 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.141991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.098641 restraints weight = 29207.765| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.32 r_work: 0.3009 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15058 Z= 0.123 Angle : 0.553 12.112 20836 Z= 0.290 Chirality : 0.038 0.309 2319 Planarity : 0.004 0.046 2319 Dihedral : 21.267 165.802 2873 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.51 % Favored : 97.42 % Rotamer: Outliers : 2.11 % Allowed : 19.76 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.22), residues: 1552 helix: 2.19 (0.17), residues: 928 sheet: 0.20 (0.63), residues: 77 loop : -0.44 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 82 TYR 0.009 0.001 TYR A 264 PHE 0.012 0.001 PHE A 802 TRP 0.016 0.001 TRP C 218 HIS 0.005 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (15057) covalent geometry : angle 0.55274 / 0.29 (20836) hydrogen bonds : bond 0.04155 / 2.77 ( 784) hydrogen bonds : angle 3.33875 / 2.38 ( 2180) Misc. bond : bond 0.00027 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 158 ARG cc_start: 0.6261 (mmp-170) cc_final: 0.5502 (mmp-170) REVERT: A 171 MET cc_start: 0.7917 (mmm) cc_final: 0.7300 (tpp) REVERT: A 461 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.8021 (t80) REVERT: A 533 TYR cc_start: 0.9489 (OUTLIER) cc_final: 0.8613 (t80) REVERT: A 757 GLU cc_start: 0.5358 (pm20) cc_final: 0.4864 (mm-30) REVERT: A 772 MET cc_start: 0.7230 (tmm) cc_final: 0.6768 (mtp) REVERT: B 97 HIS cc_start: 0.6679 (OUTLIER) cc_final: 0.5562 (m90) REVERT: B 163 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7470 (mtpt) REVERT: B 220 PHE cc_start: 0.8371 (m-80) cc_final: 0.7991 (m-10) REVERT: C 55 SER cc_start: 0.8280 (t) cc_final: 0.7713 (p) REVERT: C 127 MET cc_start: 0.7684 (mmm) cc_final: 0.7301 (mpp) REVERT: C 210 ARG cc_start: 0.8428 (ttp-170) cc_final: 0.8149 (ttp80) outliers start: 28 outliers final: 24 residues processed: 155 average time/residue: 0.1221 time to fit residues: 27.9238 Evaluate side-chains 160 residues out of total 1385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1043 MET Chi-restraints excluded: chain A residue 1071 VAL Chi-restraints excluded: chain A residue 1229 PHE Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 149 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 51 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 148 optimal weight: 30.0000 chunk 43 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN A 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.144226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.101633 restraints weight = 34334.017| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.71 r_work: 0.3027 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15058 Z= 0.109 Angle : 0.538 12.213 20836 Z= 0.283 Chirality : 0.037 0.309 2319 Planarity : 0.004 0.046 2319 Dihedral : 21.203 165.910 2873 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.58 % Favored : 97.36 % Rotamer: Outliers : 1.89 % Allowed : 19.91 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.22), residues: 1552 helix: 2.36 (0.17), residues: 921 sheet: 0.21 (0.62), residues: 77 loop : -0.31 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 82 TYR 0.009 0.001 TYR A 264 PHE 0.010 0.001 PHE A 802 TRP 0.020 0.001 TRP A1026 HIS 0.005 0.001 HIS A 920 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.11 (15057) covalent geometry : angle 0.53752 / 0.28 (20836) hydrogen bonds : bond 0.03702 / 2.45 ( 784) hydrogen bonds : angle 3.23351 / 2.30 ( 2180) Misc. bond : bond 0.00036 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3660.77 seconds wall clock time: 63 minutes 23.10 seconds (3803.10 seconds total)