Starting phenix.real_space_refine on Sun Aug 24 18:01:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b1r_15803/08_2025/8b1r_15803.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b1r_15803/08_2025/8b1r_15803.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 { model { file = "/net/cci-nas-00/data/ceres_data/8b1r_15803/08_2025/8b1r_15803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b1r_15803/08_2025/8b1r_15803.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b1r_15803/08_2025/8b1r_15803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b1r_15803/08_2025/8b1r_15803.map" } 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= 0.000 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 Mg 1 5.21 5 S 100 5.16 5 C 13863 2.51 5 N 3860 2.21 5 O 4129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 145 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21953 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 9358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9358 Classifications: {'peptide': 1170} Link IDs: {'PTRANS': 52, 'TRANS': 1117} Chain: "C" Number of atoms: 9078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9078 Classifications: {'peptide': 1121} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1053} Chain: "D" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2706 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain: "P" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "Q" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.45, per 1000 atoms: 0.20 Number of scatterers: 21953 At special positions: 0 Unit cell: (104.5, 136.4, 155.1, 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 100 16.00 Mg 1 11.99 O 4129 8.00 N 3860 7.00 C 13863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 969.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5194 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 18 sheets defined 58.1% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.608A pdb=" N THR B 32 " --> pdb=" O GLY B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 106 through 120 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.759A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.024A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.647A pdb=" N ASP B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 Processing helix chain 'B' and resid 241 through 250 removed outlier: 3.907A pdb=" N ALA B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.637A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 307 through 318 Processing helix chain 'B' and resid 323 through 347 removed outlier: 3.521A pdb=" N VAL B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.633A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.550A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.800A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 461 Processing helix chain 'B' and resid 482 through 487 removed outlier: 4.161A pdb=" N ALA B 486 " --> pdb=" O LYS B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 536 Processing helix chain 'B' and resid 560 through 574 removed outlier: 3.772A pdb=" N LEU B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 removed outlier: 3.510A pdb=" N GLU B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 589' Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.897A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.590A pdb=" N LEU B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 Processing helix chain 'B' and resid 634 through 655 removed outlier: 3.625A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 669 removed outlier: 3.701A pdb=" N MET B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 Processing helix chain 'B' and resid 679 through 700 removed outlier: 4.031A pdb=" N ARG B 683 " --> pdb=" O GLY B 679 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 717 removed outlier: 3.685A pdb=" N LEU B 707 " --> pdb=" O SER B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 745 Processing helix chain 'B' and resid 783 through 808 removed outlier: 3.680A pdb=" N LEU B 789 " --> pdb=" O GLU B 785 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG B 808 " --> pdb=" O VAL B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 835 removed outlier: 4.144A pdb=" N HIS B 834 " --> pdb=" O THR B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 844 Processing helix chain 'B' and resid 849 through 861 Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 916 through 921 Processing helix chain 'B' and resid 941 through 945 Processing helix chain 'B' and resid 948 through 961 removed outlier: 3.667A pdb=" N ASP B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 981 Processing helix chain 'B' and resid 983 through 985 No H-bonds generated for 'chain 'B' and resid 983 through 985' Processing helix chain 'B' and resid 986 through 999 removed outlier: 3.686A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 997 " --> pdb=" O TRP B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 4.061A pdb=" N GLN B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1050 Processing helix chain 'B' and resid 1089 through 1093 Processing helix chain 'B' and resid 1094 through 1106 Processing helix chain 'B' and resid 1106 through 1126 removed outlier: 4.025A pdb=" N GLN B1110 " --> pdb=" O ARG B1106 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1134 Processing helix chain 'B' and resid 1161 through 1174 Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.989A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 55 removed outlier: 3.618A pdb=" N ALA C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 87 through 103 removed outlier: 3.760A pdb=" N SER C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP C 93 " --> pdb=" O GLN C 89 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 104 through 107 removed outlier: 6.241A pdb=" N ASP C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 104 through 107' Processing helix chain 'C' and resid 108 through 116 removed outlier: 3.770A pdb=" N TYR C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.682A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 Proline residue: C 167 - end of helix removed outlier: 3.801A pdb=" N HIS C 177 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 removed outlier: 4.409A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 removed outlier: 4.066A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 282 through 287 removed outlier: 4.034A pdb=" N LEU C 286 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 282 through 287' Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 317 removed outlier: 3.745A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.669A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 414 through 428 Proline residue: C 420 - end of helix Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.712A pdb=" N GLU C 452 " --> pdb=" O HIS C 448 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER C 459 " --> pdb=" O ILE C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 476 removed outlier: 3.637A pdb=" N VAL C 476 " --> pdb=" O ALA C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 483 Processing helix chain 'C' and resid 486 through 501 removed outlier: 3.899A pdb=" N GLY C 501 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 580 removed outlier: 3.719A pdb=" N GLY C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 573 " --> pdb=" O MET C 569 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN C 580 " --> pdb=" O ARG C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 599 removed outlier: 3.608A pdb=" N ALA C 597 " --> pdb=" O ASP C 593 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE C 598 " --> pdb=" O MET C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 626 removed outlier: 4.185A pdb=" N ALA C 608 " --> pdb=" O GLU C 604 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 648 removed outlier: 3.972A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 700 removed outlier: 3.592A pdb=" N GLN C 699 " --> pdb=" O ASP C 695 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 700 " --> pdb=" O LEU C 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 695 through 700' Processing helix chain 'C' and resid 707 through 722 removed outlier: 3.885A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 768 through 780 Processing helix chain 'C' and resid 790 through 794 Processing helix chain 'C' and resid 806 through 811 Processing helix chain 'C' and resid 834 through 843 removed outlier: 3.827A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 851 removed outlier: 3.938A pdb=" N PHE C 849 " --> pdb=" O VAL C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 890 removed outlier: 3.649A pdb=" N ILE C 880 " --> pdb=" O SER C 876 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU C 890 " --> pdb=" O ASN C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 905 removed outlier: 3.881A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 934 removed outlier: 3.631A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C 933 " --> pdb=" O ASP C 929 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS C 934 " --> pdb=" O ARG C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 991 removed outlier: 3.543A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 Processing helix chain 'C' and resid 1040 through 1049 Processing helix chain 'C' and resid 1060 through 1077 Processing helix chain 'C' and resid 1087 through 1094 Processing helix chain 'C' and resid 1098 through 1120 Proline residue: C1115 - end of helix Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 65 through 71 removed outlier: 3.698A pdb=" N ALA D 69 " --> pdb=" O HIS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 76 Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.606A pdb=" N CYS D 84 " --> pdb=" O ASN D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 152 through 164 Processing helix chain 'D' and resid 176 through 192 removed outlier: 3.578A pdb=" N ALA D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 221 Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.528A pdb=" N ARG D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE D 233 " --> pdb=" O GLN D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.500A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 286 removed outlier: 3.678A pdb=" N ASP D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.563A pdb=" N VAL D 304 " --> pdb=" O GLN D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'D' and resid 315 through 319 removed outlier: 3.895A pdb=" N ASN D 318 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 334 Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'P' and resid 10 through 49 removed outlier: 3.557A pdb=" N ASN P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP P 15 " --> pdb=" O ASP P 11 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE P 16 " --> pdb=" O VAL P 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 49 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.228A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.637A pdb=" N GLN B 151 " --> pdb=" O LEU B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 208 removed outlier: 6.516A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA5, first strand: chain 'B' and resid 494 through 495 Processing sheet with id=AA6, first strand: chain 'B' and resid 578 through 581 removed outlier: 3.855A pdb=" N GLN B 737 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N TYR B 749 " --> pdb=" O VAL B 810 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N HIS B 812 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU B 751 " --> pdb=" O HIS B 812 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N SER B 814 " --> pdb=" O LEU B 751 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TRP B 753 " --> pdb=" O SER B 814 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N GLY B 816 " --> pdb=" O TRP B 753 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS B 500 " --> pdb=" O LEU B 815 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL B 817 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TRP B 502 " --> pdb=" O VAL B 817 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA B 870 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 503 " --> pdb=" O ALA B 870 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 904 through 905 removed outlier: 9.749A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE B1070 " --> pdb=" O TYR B1077 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N TYR B1076 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY B1137 " --> pdb=" O TYR B1076 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 904 through 905 removed outlier: 6.699A pdb=" N LEU B1068 " --> pdb=" O VAL B1019 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL B1019 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE B1070 " --> pdb=" O LYS B1017 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LYS B1017 " --> pdb=" O PHE B1070 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.425A pdb=" N GLU C 33 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLN C 264 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ASP C 324 " --> pdb=" O GLN C 264 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG C 266 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.045A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 437 through 439 removed outlier: 6.418A pdb=" N ALA C 438 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N THR C 663 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C 375 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 442 through 443 removed outlier: 3.724A pdb=" N ARG C 442 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 831 through 833 removed outlier: 3.845A pdb=" N THR C 953 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 956 " --> pdb=" O MET C 941 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET C 941 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 831 through 833 removed outlier: 3.845A pdb=" N THR C 953 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 14.768A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 12.514A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C1004 " --> pdb=" O LEU C1000 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1050 through 1051 removed outlier: 3.533A pdb=" N ALA C1056 " --> pdb=" O ASP C1051 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.508A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 238 through 239 removed outlier: 3.825A pdb=" N SER D 238 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA D 203 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY D 296 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 5 through 9 removed outlier: 3.543A pdb=" N ILE Q 8 " --> pdb=" O VAL P 6 " (cutoff:3.500A) 1134 hydrogen bonds defined for protein. 3324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.77 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6514 1.34 - 1.45: 3410 1.45 - 1.57: 12336 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 22428 Sorted by residual: bond pdb=" N PRO B 283 " pdb=" CD PRO B 283 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 2.02e+01 bond pdb=" N HIS B 307 " pdb=" CA HIS B 307 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.11e-02 8.12e+03 1.11e+01 bond pdb=" N VAL C 547 " pdb=" CA VAL C 547 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.19e-02 7.06e+03 1.05e+01 bond pdb=" N GLY B 302 " pdb=" CA GLY B 302 " ideal model delta sigma weight residual 1.445 1.475 -0.031 9.90e-03 1.02e+04 9.67e+00 bond pdb=" N TRP B 401 " pdb=" CA TRP B 401 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.22e-02 6.72e+03 9.55e+00 ... (remaining 22423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 29307 1.60 - 3.20: 1022 3.20 - 4.80: 96 4.80 - 6.40: 15 6.40 - 8.00: 2 Bond angle restraints: 30442 Sorted by residual: angle pdb=" N LEU B1002 " pdb=" CA LEU B1002 " pdb=" C LEU B1002 " ideal model delta sigma weight residual 111.28 116.56 -5.28 1.09e+00 8.42e-01 2.35e+01 angle pdb=" N ASN B1003 " pdb=" CA ASN B1003 " pdb=" C ASN B1003 " ideal model delta sigma weight residual 108.45 114.50 -6.05 1.26e+00 6.30e-01 2.31e+01 angle pdb=" N LEU C 600 " pdb=" CA LEU C 600 " pdb=" C LEU C 600 " ideal model delta sigma weight residual 108.69 100.69 8.00 1.80e+00 3.09e-01 1.97e+01 angle pdb=" N PHE C 599 " pdb=" CA PHE C 599 " pdb=" C PHE C 599 " ideal model delta sigma weight residual 109.24 116.59 -7.35 1.67e+00 3.59e-01 1.94e+01 angle pdb=" N PHE C 326 " pdb=" CA PHE C 326 " pdb=" C PHE C 326 " ideal model delta sigma weight residual 110.24 115.82 -5.58 1.41e+00 5.03e-01 1.57e+01 ... (remaining 30437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 12887 14.97 - 29.94: 561 29.94 - 44.92: 107 44.92 - 59.89: 28 59.89 - 74.86: 9 Dihedral angle restraints: 13592 sinusoidal: 5586 harmonic: 8006 Sorted by residual: dihedral pdb=" CA LYS B 256 " pdb=" C LYS B 256 " pdb=" N PHE B 257 " pdb=" CA PHE B 257 " ideal model delta harmonic sigma weight residual -180.00 -154.41 -25.59 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA TYR D 108 " pdb=" C TYR D 108 " pdb=" N LEU D 109 " pdb=" CA LEU D 109 " ideal model delta harmonic sigma weight residual 180.00 164.03 15.97 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA ARG C 433 " pdb=" CB ARG C 433 " pdb=" CG ARG C 433 " pdb=" CD ARG C 433 " ideal model delta sinusoidal sigma weight residual -60.00 -118.97 58.97 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 13589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2776 0.055 - 0.109: 409 0.109 - 0.164: 117 0.164 - 0.219: 34 0.219 - 0.274: 6 Chirality restraints: 3342 Sorted by residual: chirality pdb=" CA VAL Q 6 " pdb=" N VAL Q 6 " pdb=" C VAL Q 6 " pdb=" CB VAL Q 6 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL C 547 " pdb=" CA VAL C 547 " pdb=" CG1 VAL C 547 " pdb=" CG2 VAL C 547 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ILE Q 8 " pdb=" N ILE Q 8 " pdb=" C ILE Q 8 " pdb=" CB ILE Q 8 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 3339 not shown) Planarity restraints: 4015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO C 658 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG P 3 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C ARG P 3 " -0.032 2.00e-02 2.50e+03 pdb=" O ARG P 3 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP P 4 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 295 " -0.008 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C GLU B 295 " 0.030 2.00e-02 2.50e+03 pdb=" O GLU B 295 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP B 296 " -0.010 2.00e-02 2.50e+03 ... (remaining 4012 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2327 2.75 - 3.29: 21026 3.29 - 3.82: 35086 3.82 - 4.36: 41171 4.36 - 4.90: 72963 Nonbonded interactions: 172573 Sorted by model distance: nonbonded pdb=" OG1 THR B 63 " pdb=" OG1 THR B 69 " model vdw 2.210 3.040 nonbonded pdb=" NH2 ARG B 254 " pdb=" OE2 GLU Q 45 " model vdw 2.212 3.120 nonbonded pdb=" OH TYR B 394 " pdb=" OE1 GLU B 436 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR B 906 " pdb=" O ARG B1106 " model vdw 2.229 3.040 nonbonded pdb=" O TYR B1081 " pdb="MG MG B1301 " model vdw 2.286 2.170 ... (remaining 172568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.000 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22428 Z= 0.307 Angle : 0.633 7.998 30442 Z= 0.455 Chirality : 0.047 0.274 3342 Planarity : 0.004 0.055 4015 Dihedral : 9.184 74.859 8398 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.34 % Allowed : 3.50 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.15), residues: 2736 helix: 0.48 (0.13), residues: 1456 sheet: 0.80 (0.32), residues: 224 loop : -0.62 (0.17), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 734 TYR 0.020 0.001 TYR B1111 PHE 0.013 0.001 PHE C 193 TRP 0.009 0.001 TRP B 236 HIS 0.004 0.001 HIS B 402 Details of bonding type rmsd covalent geometry : bond 0.00413 (22428) covalent geometry : angle 0.63279 (30442) hydrogen bonds : bond 0.16118 ( 1131) hydrogen bonds : angle 5.45956 ( 3324) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 409 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 226 VAL cc_start: 0.9309 (t) cc_final: 0.8362 (m) REVERT: B 289 PHE cc_start: 0.8826 (m-80) cc_final: 0.8153 (m-80) REVERT: B 310 PHE cc_start: 0.8229 (m-80) cc_final: 0.7924 (m-80) REVERT: B 469 MET cc_start: 0.8942 (ptm) cc_final: 0.8707 (ptm) REVERT: B 518 MET cc_start: 0.9282 (mmm) cc_final: 0.8948 (mmm) REVERT: B 541 MET cc_start: 0.8150 (mtp) cc_final: 0.7888 (mtm) REVERT: B 902 ARG cc_start: 0.8524 (ptt180) cc_final: 0.8256 (ptt-90) REVERT: B 941 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8094 (t) REVERT: B 1102 MET cc_start: 0.8747 (mmm) cc_final: 0.8453 (mmm) REVERT: C 484 ASP cc_start: 0.8611 (t0) cc_final: 0.8324 (t0) REVERT: C 698 SER cc_start: 0.9307 (t) cc_final: 0.9054 (p) REVERT: C 1031 MET cc_start: 0.9096 (mmt) cc_final: 0.8804 (mmp) REVERT: C 1078 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7983 (p0) REVERT: D 348 LEU cc_start: 0.8699 (tp) cc_final: 0.8481 (tp) REVERT: P 24 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8656 (mt-10) REVERT: P 33 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8305 (tm-30) REVERT: Q 15 ASP cc_start: 0.8465 (m-30) cc_final: 0.8071 (m-30) REVERT: Q 40 TYR cc_start: 0.8062 (t80) cc_final: 0.7859 (t80) outliers start: 8 outliers final: 3 residues processed: 415 average time/residue: 0.1792 time to fit residues: 107.8834 Evaluate side-chains 212 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 207 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain C residue 1078 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN B 258 ASN B 403 HIS B1153 GLN C 792 GLN C 960 GLN C1073 GLN ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 ASN Q 14 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.096044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.064501 restraints weight = 42610.329| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.75 r_work: 0.2603 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22428 Z= 0.203 Angle : 0.548 8.127 30442 Z= 0.282 Chirality : 0.041 0.176 3342 Planarity : 0.005 0.050 4015 Dihedral : 3.742 48.980 3024 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.28 % Allowed : 7.33 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.15), residues: 2736 helix: 1.73 (0.13), residues: 1455 sheet: 1.24 (0.33), residues: 213 loop : -0.28 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 25 TYR 0.027 0.002 TYR B1111 PHE 0.018 0.002 PHE C 193 TRP 0.013 0.001 TRP P 13 HIS 0.004 0.001 HIS B 772 Details of bonding type rmsd covalent geometry : bond 0.00482 (22428) covalent geometry : angle 0.54789 (30442) hydrogen bonds : bond 0.05166 ( 1131) hydrogen bonds : angle 4.22740 ( 3324) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 321 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8834 (pp) REVERT: B 469 MET cc_start: 0.9181 (ptm) cc_final: 0.8967 (ptm) REVERT: B 541 MET cc_start: 0.8880 (mtp) cc_final: 0.8406 (mtp) REVERT: B 902 ARG cc_start: 0.9030 (ptt180) cc_final: 0.8609 (ptt-90) REVERT: B 1021 MET cc_start: 0.9143 (ttm) cc_final: 0.8870 (ttp) REVERT: B 1102 MET cc_start: 0.8947 (mmm) cc_final: 0.8659 (mmm) REVERT: C 266 ARG cc_start: 0.8110 (ptm160) cc_final: 0.7849 (ptm160) REVERT: C 281 GLU cc_start: 0.8293 (mp0) cc_final: 0.8004 (mp0) REVERT: D 218 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6687 (mmtm) REVERT: P 28 ASP cc_start: 0.8853 (m-30) cc_final: 0.8539 (m-30) REVERT: P 31 LYS cc_start: 0.8920 (mmtm) cc_final: 0.8500 (mmtm) REVERT: P 33 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8297 (tm-30) REVERT: Q 11 ASP cc_start: 0.8520 (m-30) cc_final: 0.8125 (m-30) REVERT: Q 15 ASP cc_start: 0.8544 (m-30) cc_final: 0.8020 (m-30) REVERT: Q 24 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8126 (mt-10) REVERT: Q 30 LEU cc_start: 0.8670 (mm) cc_final: 0.8417 (mt) REVERT: Q 34 LEU cc_start: 0.8439 (tt) cc_final: 0.7945 (tt) REVERT: Q 39 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7621 (pp20) outliers start: 30 outliers final: 10 residues processed: 227 average time/residue: 0.1543 time to fit residues: 52.9841 Evaluate side-chains 187 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain Q residue 39 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 149 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 264 optimal weight: 5.9990 chunk 108 optimal weight: 0.0470 chunk 150 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1057 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.096944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.067672 restraints weight = 42173.875| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.57 r_work: 0.2656 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22428 Z= 0.119 Angle : 0.472 15.165 30442 Z= 0.238 Chirality : 0.038 0.141 3342 Planarity : 0.004 0.054 4015 Dihedral : 3.598 46.658 3021 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.94 % Allowed : 8.32 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.16), residues: 2736 helix: 2.23 (0.13), residues: 1461 sheet: 1.29 (0.34), residues: 210 loop : -0.18 (0.17), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 25 TYR 0.024 0.001 TYR B1111 PHE 0.017 0.001 PHE B 289 TRP 0.013 0.001 TRP C 616 HIS 0.003 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00273 (22428) covalent geometry : angle 0.47226 (30442) hydrogen bonds : bond 0.04093 ( 1131) hydrogen bonds : angle 3.89197 ( 3324) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.8827 (mtpp) cc_final: 0.8494 (ptpp) REVERT: B 321 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8875 (pp) REVERT: B 390 ASP cc_start: 0.8089 (t0) cc_final: 0.7823 (t0) REVERT: B 469 MET cc_start: 0.9132 (ptm) cc_final: 0.8917 (ptm) REVERT: B 541 MET cc_start: 0.8812 (mtp) cc_final: 0.8578 (mtp) REVERT: B 902 ARG cc_start: 0.8996 (ptt180) cc_final: 0.8603 (ptt-90) REVERT: B 1021 MET cc_start: 0.9099 (ttm) cc_final: 0.8855 (ttp) REVERT: B 1102 MET cc_start: 0.8947 (mmm) cc_final: 0.8652 (mmm) REVERT: C 266 ARG cc_start: 0.8101 (ptm160) cc_final: 0.7360 (ttt90) REVERT: C 281 GLU cc_start: 0.8250 (mp0) cc_final: 0.7937 (mp0) REVERT: C 288 ASN cc_start: 0.7761 (t0) cc_final: 0.7467 (m-40) REVERT: P 33 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8293 (tm-30) REVERT: Q 24 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8225 (mt-10) REVERT: Q 33 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.8048 (mm-40) REVERT: Q 34 LEU cc_start: 0.8392 (tt) cc_final: 0.8138 (tt) outliers start: 22 outliers final: 9 residues processed: 205 average time/residue: 0.1518 time to fit residues: 48.2261 Evaluate side-chains 189 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 316 ASP Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain Q residue 33 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 66 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 152 optimal weight: 0.0570 chunk 240 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 236 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 137 optimal weight: 0.0050 chunk 25 optimal weight: 5.9990 chunk 270 optimal weight: 10.0000 overall best weight: 2.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 GLN C 724 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.064589 restraints weight = 42598.255| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.70 r_work: 0.2595 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22428 Z= 0.157 Angle : 0.482 13.578 30442 Z= 0.244 Chirality : 0.039 0.147 3342 Planarity : 0.004 0.050 4015 Dihedral : 3.547 35.595 3018 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.11 % Allowed : 8.32 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.16), residues: 2736 helix: 2.38 (0.13), residues: 1465 sheet: 1.08 (0.33), residues: 225 loop : -0.16 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 25 TYR 0.025 0.001 TYR B1111 PHE 0.016 0.001 PHE C 193 TRP 0.012 0.001 TRP C 616 HIS 0.003 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00374 (22428) covalent geometry : angle 0.48237 (30442) hydrogen bonds : bond 0.04424 ( 1131) hydrogen bonds : angle 3.93057 ( 3324) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.8812 (mtpp) cc_final: 0.8454 (ptpp) REVERT: B 321 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8857 (pp) REVERT: B 390 ASP cc_start: 0.8201 (t0) cc_final: 0.7848 (t0) REVERT: B 541 MET cc_start: 0.8967 (mtp) cc_final: 0.8724 (mtp) REVERT: B 823 ARG cc_start: 0.7271 (ttm170) cc_final: 0.6737 (mmm-85) REVERT: B 902 ARG cc_start: 0.9004 (ptt180) cc_final: 0.8628 (ptt-90) REVERT: B 1021 MET cc_start: 0.9131 (ttm) cc_final: 0.8892 (ttp) REVERT: B 1102 MET cc_start: 0.8976 (mmm) cc_final: 0.8734 (mtp) REVERT: C 266 ARG cc_start: 0.8070 (ptm160) cc_final: 0.7399 (ttt90) REVERT: C 281 GLU cc_start: 0.8308 (mp0) cc_final: 0.7961 (mp0) REVERT: C 288 ASN cc_start: 0.7708 (t0) cc_final: 0.7446 (m-40) REVERT: C 667 MET cc_start: 0.9466 (mmt) cc_final: 0.9009 (mmt) REVERT: C 962 ASP cc_start: 0.8530 (t0) cc_final: 0.8036 (t0) REVERT: D 184 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7947 (mm) REVERT: D 218 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6798 (mmtm) REVERT: P 33 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8259 (tm-30) REVERT: Q 24 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8327 (mt-10) REVERT: Q 33 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8058 (mm-40) outliers start: 26 outliers final: 10 residues processed: 202 average time/residue: 0.1480 time to fit residues: 45.9286 Evaluate side-chains 186 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 33 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 21 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 30.0000 chunk 1 optimal weight: 0.0020 chunk 179 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.094511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.063884 restraints weight = 42391.697| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.68 r_work: 0.2590 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22428 Z= 0.165 Angle : 0.496 13.952 30442 Z= 0.250 Chirality : 0.039 0.188 3342 Planarity : 0.004 0.048 4015 Dihedral : 3.620 38.554 3018 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.02 % Allowed : 8.87 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.16), residues: 2736 helix: 2.41 (0.13), residues: 1469 sheet: 1.02 (0.33), residues: 230 loop : -0.16 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 25 TYR 0.025 0.001 TYR B1111 PHE 0.024 0.001 PHE B 31 TRP 0.013 0.001 TRP C 616 HIS 0.006 0.001 HIS B 914 Details of bonding type rmsd covalent geometry : bond 0.00395 (22428) covalent geometry : angle 0.49605 (30442) hydrogen bonds : bond 0.04437 ( 1131) hydrogen bonds : angle 3.93678 ( 3324) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.8759 (mtpp) cc_final: 0.8510 (ptpp) REVERT: B 321 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8879 (pp) REVERT: B 390 ASP cc_start: 0.8258 (t0) cc_final: 0.7902 (t0) REVERT: B 541 MET cc_start: 0.9031 (mtp) cc_final: 0.8743 (mtp) REVERT: B 823 ARG cc_start: 0.7039 (ttm170) cc_final: 0.6500 (mmm-85) REVERT: B 902 ARG cc_start: 0.8982 (ptt180) cc_final: 0.8634 (ptt-90) REVERT: B 1021 MET cc_start: 0.9144 (ttm) cc_final: 0.8941 (ttp) REVERT: B 1102 MET cc_start: 0.8988 (mmm) cc_final: 0.8739 (mtp) REVERT: C 14 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7898 (tm-30) REVERT: C 266 ARG cc_start: 0.8067 (ptm160) cc_final: 0.7457 (ttt90) REVERT: C 281 GLU cc_start: 0.8299 (mp0) cc_final: 0.7940 (mp0) REVERT: C 288 ASN cc_start: 0.7706 (t0) cc_final: 0.7466 (m-40) REVERT: C 667 MET cc_start: 0.9489 (mmt) cc_final: 0.9162 (mmt) REVERT: C 962 ASP cc_start: 0.8535 (t0) cc_final: 0.8068 (t0) REVERT: D 184 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7789 (mm) REVERT: D 218 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6802 (mmtm) REVERT: P 19 TYR cc_start: 0.9191 (t80) cc_final: 0.8930 (t80) REVERT: P 30 LEU cc_start: 0.9169 (mt) cc_final: 0.8944 (mt) REVERT: P 33 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8447 (tm-30) REVERT: P 36 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8894 (mt-10) REVERT: Q 24 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8307 (mt-10) REVERT: Q 33 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.8064 (mm-40) outliers start: 24 outliers final: 12 residues processed: 195 average time/residue: 0.1386 time to fit residues: 42.2152 Evaluate side-chains 181 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 33 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 94 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 263 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.095174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.064410 restraints weight = 42490.909| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.70 r_work: 0.2605 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22428 Z= 0.122 Angle : 0.456 6.467 30442 Z= 0.233 Chirality : 0.038 0.139 3342 Planarity : 0.004 0.047 4015 Dihedral : 3.524 36.047 3018 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.41 % Allowed : 8.49 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.16), residues: 2736 helix: 2.53 (0.13), residues: 1468 sheet: 1.09 (0.33), residues: 236 loop : -0.14 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 25 TYR 0.024 0.001 TYR B1111 PHE 0.018 0.001 PHE B 31 TRP 0.017 0.001 TRP B 265 HIS 0.003 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00287 (22428) covalent geometry : angle 0.45594 (30442) hydrogen bonds : bond 0.03924 ( 1131) hydrogen bonds : angle 3.80357 ( 3324) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.8909 (mmm) cc_final: 0.8423 (tpp) REVERT: B 264 LYS cc_start: 0.8773 (mtpp) cc_final: 0.8494 (ptpp) REVERT: B 321 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8848 (pp) REVERT: B 541 MET cc_start: 0.9009 (mtp) cc_final: 0.8696 (mtp) REVERT: B 587 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8857 (p) REVERT: B 823 ARG cc_start: 0.7024 (ttm170) cc_final: 0.6420 (mmm-85) REVERT: B 902 ARG cc_start: 0.8979 (ptt180) cc_final: 0.8620 (ptt-90) REVERT: B 1061 MET cc_start: 0.9105 (mmt) cc_final: 0.8905 (mmt) REVERT: B 1102 MET cc_start: 0.8969 (mmm) cc_final: 0.8231 (mtp) REVERT: C 14 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7849 (tm-30) REVERT: C 266 ARG cc_start: 0.8055 (ptm160) cc_final: 0.7460 (ttt90) REVERT: C 281 GLU cc_start: 0.8291 (mp0) cc_final: 0.7987 (mp0) REVERT: C 288 ASN cc_start: 0.7694 (t0) cc_final: 0.7470 (m-40) REVERT: C 667 MET cc_start: 0.9508 (mmt) cc_final: 0.9243 (mmt) REVERT: C 962 ASP cc_start: 0.8553 (t0) cc_final: 0.8085 (t0) REVERT: D 184 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7880 (mm) REVERT: D 218 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6699 (mmmt) REVERT: P 30 LEU cc_start: 0.9189 (mt) cc_final: 0.8980 (mt) REVERT: P 33 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8270 (tm-30) REVERT: Q 3 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7776 (mmm160) REVERT: Q 17 GLN cc_start: 0.9324 (mm110) cc_final: 0.9045 (mm-40) REVERT: Q 24 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8248 (mt-10) REVERT: Q 33 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.8012 (mm-40) outliers start: 33 outliers final: 16 residues processed: 203 average time/residue: 0.1479 time to fit residues: 46.1967 Evaluate side-chains 191 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 33 GLN Chi-restraints excluded: chain Q residue 39 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 chunk 200 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 121 optimal weight: 0.0010 chunk 156 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.095785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.065272 restraints weight = 42351.125| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.70 r_work: 0.2612 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22428 Z= 0.106 Angle : 0.453 8.461 30442 Z= 0.229 Chirality : 0.037 0.139 3342 Planarity : 0.004 0.050 4015 Dihedral : 3.454 33.872 3018 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.19 % Allowed : 8.83 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.16), residues: 2736 helix: 2.61 (0.14), residues: 1471 sheet: 1.18 (0.34), residues: 237 loop : -0.08 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 25 TYR 0.023 0.001 TYR B1111 PHE 0.018 0.001 PHE B 31 TRP 0.020 0.001 TRP B 265 HIS 0.003 0.000 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00243 (22428) covalent geometry : angle 0.45261 (30442) hydrogen bonds : bond 0.03664 ( 1131) hydrogen bonds : angle 3.72157 ( 3324) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8889 (pp) REVERT: B 541 MET cc_start: 0.9005 (mtp) cc_final: 0.8730 (mtp) REVERT: B 823 ARG cc_start: 0.7032 (ttm170) cc_final: 0.6535 (mmm-85) REVERT: B 902 ARG cc_start: 0.8977 (ptt180) cc_final: 0.8619 (ptt-90) REVERT: B 1102 MET cc_start: 0.8970 (mmm) cc_final: 0.8746 (mtp) REVERT: C 266 ARG cc_start: 0.8057 (ptm160) cc_final: 0.7438 (ttt90) REVERT: C 281 GLU cc_start: 0.8312 (mp0) cc_final: 0.8008 (mp0) REVERT: C 288 ASN cc_start: 0.7677 (t0) cc_final: 0.7473 (m-40) REVERT: C 667 MET cc_start: 0.9508 (mmt) cc_final: 0.9250 (mmt) REVERT: C 962 ASP cc_start: 0.8555 (t0) cc_final: 0.8081 (t0) REVERT: C 1017 LEU cc_start: 0.9310 (mt) cc_final: 0.9098 (mt) REVERT: D 184 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7802 (mm) REVERT: D 218 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6598 (mmmt) REVERT: P 30 LEU cc_start: 0.9240 (mt) cc_final: 0.8952 (mt) REVERT: P 33 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8322 (tm-30) REVERT: P 36 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8988 (tm-30) REVERT: P 38 ASP cc_start: 0.8641 (m-30) cc_final: 0.8363 (p0) REVERT: Q 3 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7822 (mmm160) REVERT: Q 17 GLN cc_start: 0.9311 (mm110) cc_final: 0.9100 (mm-40) REVERT: Q 24 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8453 (mt-10) REVERT: Q 33 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8093 (mm-40) outliers start: 28 outliers final: 15 residues processed: 196 average time/residue: 0.1562 time to fit residues: 46.8307 Evaluate side-chains 187 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 33 GLN Chi-restraints excluded: chain Q residue 39 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 20 optimal weight: 0.0270 chunk 176 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 236 optimal weight: 0.8980 chunk 2 optimal weight: 0.0070 chunk 107 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.3860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 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 = 0.3333 r_free = 0.3333 target = 0.095578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.066129 restraints weight = 41795.129| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.59 r_work: 0.2620 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22428 Z= 0.108 Angle : 0.450 7.597 30442 Z= 0.229 Chirality : 0.037 0.136 3342 Planarity : 0.004 0.059 4015 Dihedral : 3.418 32.280 3018 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.24 % Allowed : 8.83 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.16), residues: 2736 helix: 2.64 (0.13), residues: 1474 sheet: 1.32 (0.34), residues: 235 loop : -0.05 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Q 25 TYR 0.023 0.001 TYR B1111 PHE 0.017 0.001 PHE B 31 TRP 0.021 0.001 TRP B 265 HIS 0.003 0.000 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00250 (22428) covalent geometry : angle 0.44970 (30442) hydrogen bonds : bond 0.03639 ( 1131) hydrogen bonds : angle 3.69272 ( 3324) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8905 (pp) REVERT: B 541 MET cc_start: 0.9008 (mtp) cc_final: 0.8708 (mtp) REVERT: B 823 ARG cc_start: 0.6984 (ttm170) cc_final: 0.6535 (mmm-85) REVERT: B 902 ARG cc_start: 0.8965 (ptt180) cc_final: 0.8616 (ptt-90) REVERT: B 1102 MET cc_start: 0.8957 (mmm) cc_final: 0.8709 (mtp) REVERT: C 266 ARG cc_start: 0.8080 (ptm160) cc_final: 0.7481 (ttt90) REVERT: C 281 GLU cc_start: 0.8313 (mp0) cc_final: 0.8015 (mp0) REVERT: C 962 ASP cc_start: 0.8632 (t0) cc_final: 0.8191 (t0) REVERT: C 1017 LEU cc_start: 0.9315 (mt) cc_final: 0.9096 (mt) REVERT: D 184 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7905 (mm) REVERT: D 218 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6620 (mmmt) REVERT: P 30 LEU cc_start: 0.9287 (mt) cc_final: 0.9020 (mt) REVERT: P 31 LYS cc_start: 0.8828 (mmtm) cc_final: 0.8569 (mmtm) REVERT: P 33 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8518 (tm-30) REVERT: Q 3 ARG cc_start: 0.8136 (mmm160) cc_final: 0.7848 (mmm160) REVERT: Q 24 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8410 (mt-10) REVERT: Q 30 LEU cc_start: 0.8934 (tp) cc_final: 0.8719 (tt) REVERT: Q 33 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8076 (mm-40) outliers start: 29 outliers final: 19 residues processed: 194 average time/residue: 0.1564 time to fit residues: 46.6501 Evaluate side-chains 189 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 33 GLN Chi-restraints excluded: chain Q residue 39 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 106 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 260 optimal weight: 0.4980 chunk 26 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 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 = 0.3324 r_free = 0.3324 target = 0.094806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.065529 restraints weight = 42096.944| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.57 r_work: 0.2608 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22428 Z= 0.127 Angle : 0.466 9.787 30442 Z= 0.235 Chirality : 0.038 0.135 3342 Planarity : 0.004 0.058 4015 Dihedral : 3.465 34.911 3018 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.11 % Allowed : 8.96 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.16), residues: 2736 helix: 2.64 (0.14), residues: 1474 sheet: 1.28 (0.34), residues: 237 loop : -0.06 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Q 25 TYR 0.023 0.001 TYR B1111 PHE 0.028 0.001 PHE B 293 TRP 0.018 0.001 TRP B 265 HIS 0.003 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00302 (22428) covalent geometry : angle 0.46557 (30442) hydrogen bonds : bond 0.03851 ( 1131) hydrogen bonds : angle 3.73958 ( 3324) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8962 (pp) REVERT: B 541 MET cc_start: 0.9232 (mtp) cc_final: 0.8918 (mtp) REVERT: B 823 ARG cc_start: 0.7283 (ttm170) cc_final: 0.6789 (mmm-85) REVERT: B 902 ARG cc_start: 0.9104 (ptt180) cc_final: 0.8747 (ptt-90) REVERT: B 1102 MET cc_start: 0.9093 (mmm) cc_final: 0.8848 (mtp) REVERT: C 253 ASP cc_start: 0.8217 (t0) cc_final: 0.7990 (t0) REVERT: C 266 ARG cc_start: 0.8138 (ptm160) cc_final: 0.7524 (ttt90) REVERT: C 281 GLU cc_start: 0.8465 (mp0) cc_final: 0.8163 (mp0) REVERT: C 962 ASP cc_start: 0.8843 (t0) cc_final: 0.8405 (t0) REVERT: C 1017 LEU cc_start: 0.9371 (mt) cc_final: 0.9158 (mt) REVERT: D 160 VAL cc_start: 0.8159 (t) cc_final: 0.7924 (p) REVERT: D 184 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7879 (mm) REVERT: D 218 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6717 (mmmt) REVERT: P 30 LEU cc_start: 0.9278 (mt) cc_final: 0.9009 (mt) REVERT: P 31 LYS cc_start: 0.8808 (mmtm) cc_final: 0.8604 (mmtm) REVERT: P 33 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8257 (tm-30) REVERT: Q 3 ARG cc_start: 0.8165 (mmm160) cc_final: 0.7865 (mmm160) REVERT: Q 24 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8558 (mt-10) REVERT: Q 30 LEU cc_start: 0.8882 (tp) cc_final: 0.8665 (tt) REVERT: Q 33 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.8044 (mm-40) REVERT: Q 34 LEU cc_start: 0.8493 (tt) cc_final: 0.8237 (tt) outliers start: 26 outliers final: 20 residues processed: 189 average time/residue: 0.1557 time to fit residues: 45.1337 Evaluate side-chains 191 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 5 LEU Chi-restraints excluded: chain Q residue 33 GLN Chi-restraints excluded: chain Q residue 39 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 36 optimal weight: 7.9990 chunk 90 optimal weight: 0.0270 chunk 138 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 183 optimal weight: 0.0170 chunk 252 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 chunk 175 optimal weight: 0.0570 chunk 256 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 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 = 0.3343 r_free = 0.3343 target = 0.096225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.066879 restraints weight = 41907.032| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.59 r_work: 0.2643 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 22428 Z= 0.091 Angle : 0.449 9.335 30442 Z= 0.227 Chirality : 0.037 0.152 3342 Planarity : 0.004 0.063 4015 Dihedral : 3.362 32.094 3018 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.98 % Allowed : 9.34 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.16), residues: 2736 helix: 2.74 (0.13), residues: 1462 sheet: 1.42 (0.35), residues: 235 loop : 0.01 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG Q 25 TYR 0.022 0.001 TYR B1111 PHE 0.021 0.001 PHE B 31 TRP 0.017 0.001 TRP B 265 HIS 0.002 0.000 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00201 (22428) covalent geometry : angle 0.44881 (30442) hydrogen bonds : bond 0.03311 ( 1131) hydrogen bonds : angle 3.61050 ( 3324) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5472 Ramachandran restraints generated. 2736 Oldfield, 0 Emsley, 2736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8898 (pp) REVERT: B 541 MET cc_start: 0.8973 (mtp) cc_final: 0.8656 (mtp) REVERT: B 823 ARG cc_start: 0.7133 (ttm170) cc_final: 0.6660 (mmm-85) REVERT: B 902 ARG cc_start: 0.8939 (ptt180) cc_final: 0.8598 (ptt-90) REVERT: B 1102 MET cc_start: 0.8942 (mmm) cc_final: 0.8727 (mtp) REVERT: C 266 ARG cc_start: 0.8075 (ptm160) cc_final: 0.7469 (ttt90) REVERT: C 281 GLU cc_start: 0.8333 (mp0) cc_final: 0.8039 (mp0) REVERT: C 962 ASP cc_start: 0.8606 (t0) cc_final: 0.8146 (t0) REVERT: C 1017 LEU cc_start: 0.9314 (mt) cc_final: 0.9091 (mt) REVERT: D 160 VAL cc_start: 0.8100 (t) cc_final: 0.7862 (p) REVERT: D 218 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6654 (mmmt) REVERT: D 321 PHE cc_start: 0.5473 (m-80) cc_final: 0.5272 (m-10) REVERT: P 30 LEU cc_start: 0.9254 (mt) cc_final: 0.8872 (mt) REVERT: P 31 LYS cc_start: 0.8804 (mmtm) cc_final: 0.8567 (mmtm) REVERT: P 33 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8417 (tm-30) REVERT: P 36 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8962 (mt-10) REVERT: Q 3 ARG cc_start: 0.8174 (mmm160) cc_final: 0.7921 (mmm160) REVERT: Q 24 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8459 (mt-10) REVERT: Q 30 LEU cc_start: 0.8726 (tp) cc_final: 0.8487 (tt) outliers start: 23 outliers final: 16 residues processed: 195 average time/residue: 0.1641 time to fit residues: 48.7397 Evaluate side-chains 189 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain C residue 1072 LEU Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain Q residue 39 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 17 optimal weight: 6.9990 chunk 265 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 250 optimal weight: 30.0000 chunk 184 optimal weight: 0.7980 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.092027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.062675 restraints weight = 42469.454| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.56 r_work: 0.2542 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2398 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 22428 Z= 0.266 Angle : 0.569 14.192 30442 Z= 0.288 Chirality : 0.041 0.141 3342 Planarity : 0.005 0.064 4015 Dihedral : 3.733 36.642 3018 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.77 % Allowed : 9.89 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.16), residues: 2736 helix: 2.45 (0.13), residues: 1464 sheet: 1.23 (0.34), residues: 237 loop : -0.16 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Q 25 TYR 0.026 0.002 TYR B1111 PHE 0.025 0.002 PHE B 293 TRP 0.015 0.002 TRP B 265 HIS 0.005 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00644 (22428) covalent geometry : angle 0.56873 (30442) hydrogen bonds : bond 0.05113 ( 1131) hydrogen bonds : angle 4.09011 ( 3324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4163.08 seconds wall clock time: 72 minutes 7.48 seconds (4327.48 seconds total)