Starting phenix.real_space_refine on Wed Jun 18 23:53:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b1r_15803/06_2025/8b1r_15803.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b1r_15803/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8b1r_15803/06_2025/8b1r_15803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b1r_15803/06_2025/8b1r_15803.map" model { file = "/net/cci-nas-00/data/ceres_data/8b1r_15803/06_2025/8b1r_15803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b1r_15803/06_2025/8b1r_15803.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.89, per 1000 atoms: 0.77 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: 5.63 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.80 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: 9.22 Time building geometry restraints manager: 6.51 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: 1.090 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: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 55.740 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.430 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (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 TRP 0.009 0.001 TRP B 236 HIS 0.004 0.001 HIS B 402 PHE 0.013 0.001 PHE C 193 TYR 0.020 0.001 TYR B1111 ARG 0.003 0.000 ARG C 734 Details of bonding type rmsd hydrogen bonds : bond 0.16118 ( 1131) hydrogen bonds : angle 5.45956 ( 3324) covalent geometry : bond 0.00413 (22428) covalent geometry : angle 0.63279 (30442) *********************** 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 : 2.570 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: 0.4217 time to fit residues: 252.8361 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 : 2.619 ------------------------------------------------------------------------------- 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 229 optimal weight: 7.9990 chunk 206 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 139 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 213 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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 B 594 GLN B1153 GLN C 792 GLN C 960 GLN C1073 GLN ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 HIS P 14 ASN Q 14 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.097322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.065931 restraints weight = 42269.284| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.74 r_work: 0.2627 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22428 Z= 0.166 Angle : 0.523 8.063 30442 Z= 0.269 Chirality : 0.040 0.176 3342 Planarity : 0.004 0.050 4015 Dihedral : 3.642 48.587 3024 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.24 % Allowed : 7.25 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.15), residues: 2736 helix: 1.76 (0.13), residues: 1456 sheet: 1.27 (0.33), residues: 213 loop : -0.26 (0.17), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 13 HIS 0.003 0.001 HIS B 403 PHE 0.016 0.002 PHE C 193 TYR 0.026 0.001 TYR B1111 ARG 0.007 0.001 ARG Q 25 Details of bonding type rmsd hydrogen bonds : bond 0.04846 ( 1131) hydrogen bonds : angle 4.14422 ( 3324) covalent geometry : bond 0.00390 (22428) covalent geometry : angle 0.52291 (30442) *********************** 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 245 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 289 PHE cc_start: 0.8730 (m-80) cc_final: 0.8507 (m-80) REVERT: B 321 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8818 (pp) REVERT: B 469 MET cc_start: 0.9169 (ptm) cc_final: 0.8951 (ptm) REVERT: B 788 ASP cc_start: 0.8642 (m-30) cc_final: 0.8440 (m-30) REVERT: B 902 ARG cc_start: 0.9028 (ptt180) cc_final: 0.8610 (ptt-90) REVERT: B 1021 MET cc_start: 0.9128 (ttm) cc_final: 0.8841 (ttp) REVERT: B 1102 MET cc_start: 0.8933 (mmm) cc_final: 0.8649 (mmm) REVERT: C 266 ARG cc_start: 0.8096 (ptm160) cc_final: 0.7829 (ptm160) REVERT: C 281 GLU cc_start: 0.8318 (mp0) cc_final: 0.8021 (mp0) REVERT: C 462 ASP cc_start: 0.7499 (p0) cc_final: 0.7296 (p0) REVERT: D 218 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6632 (mmtm) REVERT: P 28 ASP cc_start: 0.8863 (m-30) cc_final: 0.8528 (m-30) REVERT: P 31 LYS cc_start: 0.8898 (mmtm) cc_final: 0.8488 (mmtm) REVERT: P 33 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8286 (tm-30) REVERT: Q 24 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8112 (mt-10) REVERT: Q 30 LEU cc_start: 0.8679 (mm) cc_final: 0.8417 (mt) REVERT: Q 32 ASN cc_start: 0.8187 (p0) cc_final: 0.7887 (p0) REVERT: Q 33 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8180 (mp10) REVERT: Q 34 LEU cc_start: 0.8422 (tt) cc_final: 0.8042 (tt) REVERT: Q 39 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7612 (pp20) outliers start: 29 outliers final: 10 residues processed: 234 average time/residue: 0.3708 time to fit residues: 134.3155 Evaluate side-chains 192 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 2.348 ------------------------------------------------------------------------------- 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 238 LEU 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 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 15 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 220 optimal weight: 10.0000 chunk 259 optimal weight: 5.9990 chunk 108 optimal weight: 0.0170 chunk 257 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.099566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.069139 restraints weight = 42138.528| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.68 r_work: 0.2688 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22428 Z= 0.094 Angle : 0.457 14.459 30442 Z= 0.228 Chirality : 0.037 0.145 3342 Planarity : 0.004 0.054 4015 Dihedral : 3.369 40.006 3019 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.85 % Allowed : 8.32 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.15), residues: 2736 helix: 2.26 (0.13), residues: 1461 sheet: 1.22 (0.33), residues: 220 loop : -0.10 (0.17), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 616 HIS 0.003 0.000 HIS B 222 PHE 0.013 0.001 PHE C 193 TYR 0.023 0.001 TYR B1111 ARG 0.010 0.000 ARG Q 25 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 1131) hydrogen bonds : angle 3.79770 ( 3324) covalent geometry : bond 0.00198 (22428) covalent geometry : angle 0.45743 (30442) *********************** 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: 20 poor density : 191 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8472 (ptpp) REVERT: B 289 PHE cc_start: 0.8640 (m-80) cc_final: 0.8236 (m-80) REVERT: B 321 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8869 (pp) REVERT: B 390 ASP cc_start: 0.8137 (t0) cc_final: 0.7854 (t0) REVERT: B 469 MET cc_start: 0.9125 (ptm) cc_final: 0.8892 (ptm) REVERT: B 541 MET cc_start: 0.8743 (mtp) cc_final: 0.8355 (mtm) REVERT: B 902 ARG cc_start: 0.9015 (ptt180) cc_final: 0.8612 (ptt-90) REVERT: B 1021 MET cc_start: 0.9104 (ttm) cc_final: 0.8857 (ttp) REVERT: B 1102 MET cc_start: 0.8903 (mmm) cc_final: 0.8662 (mmm) REVERT: C 110 LEU cc_start: 0.8997 (tt) cc_final: 0.8713 (tt) REVERT: C 266 ARG cc_start: 0.8059 (ptm160) cc_final: 0.7257 (ttt90) REVERT: C 281 GLU cc_start: 0.8231 (mp0) cc_final: 0.7916 (mp0) REVERT: D 61 ASN cc_start: 0.8071 (m-40) cc_final: 0.7796 (m110) REVERT: D 218 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6729 (mmtm) REVERT: P 30 LEU cc_start: 0.9153 (mt) cc_final: 0.8798 (mt) REVERT: P 31 LYS cc_start: 0.8810 (mmtm) cc_final: 0.8575 (mmtm) REVERT: P 33 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8416 (tm-30) REVERT: Q 24 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8217 (mt-10) REVERT: Q 33 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8233 (mm-40) outliers start: 20 outliers final: 6 residues processed: 207 average time/residue: 0.3885 time to fit residues: 124.3098 Evaluate side-chains 184 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 2.393 ------------------------------------------------------------------------------- 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 189 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain Q residue 30 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 245 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 250 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 119 optimal weight: 0.0770 overall best weight: 3.4146 ------------------------------------------------------------------------------- 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 = 0.3312 r_free = 0.3312 target = 0.094197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.063274 restraints weight = 42944.482| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.70 r_work: 0.2567 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 22428 Z= 0.211 Angle : 0.530 13.712 30442 Z= 0.269 Chirality : 0.040 0.142 3342 Planarity : 0.004 0.047 4015 Dihedral : 3.707 40.456 3018 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.07 % Allowed : 8.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.16), residues: 2736 helix: 2.31 (0.13), residues: 1459 sheet: 1.27 (0.33), residues: 215 loop : -0.19 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 616 HIS 0.006 0.001 HIS B 914 PHE 0.018 0.002 PHE C 193 TYR 0.026 0.002 TYR B1111 ARG 0.011 0.001 ARG Q 25 Details of bonding type rmsd hydrogen bonds : bond 0.05097 ( 1131) hydrogen bonds : angle 4.09945 ( 3324) covalent geometry : bond 0.00507 (22428) covalent geometry : angle 0.52956 (30442) *********************** 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 206 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.8732 (mtpp) cc_final: 0.8449 (ptpp) REVERT: B 321 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8850 (pp) REVERT: B 469 MET cc_start: 0.9165 (ptm) cc_final: 0.8964 (ptm) REVERT: B 541 MET cc_start: 0.9052 (mtp) cc_final: 0.8791 (mtp) REVERT: B 823 ARG cc_start: 0.7312 (ttm170) cc_final: 0.6783 (mmm-85) REVERT: B 902 ARG cc_start: 0.9001 (ptt180) cc_final: 0.8621 (ptt-90) REVERT: B 1021 MET cc_start: 0.9162 (ttm) cc_final: 0.8917 (ttp) REVERT: B 1102 MET cc_start: 0.9004 (mmm) cc_final: 0.8684 (mmm) REVERT: C 266 ARG cc_start: 0.8055 (ptm160) cc_final: 0.7404 (ttt90) REVERT: C 281 GLU cc_start: 0.8303 (mp0) cc_final: 0.7959 (mp0) REVERT: C 288 ASN cc_start: 0.7718 (t0) cc_final: 0.7443 (m-40) REVERT: C 659 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8718 (t) REVERT: C 962 ASP cc_start: 0.8552 (t0) cc_final: 0.8063 (t0) REVERT: D 184 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7883 (mm) REVERT: P 30 LEU cc_start: 0.9205 (mt) cc_final: 0.8821 (mt) REVERT: P 31 LYS cc_start: 0.8862 (mmtm) cc_final: 0.8642 (mmtm) REVERT: P 33 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8183 (tm-30) REVERT: Q 24 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8276 (mt-10) REVERT: Q 30 LEU cc_start: 0.8564 (mm) cc_final: 0.8334 (mt) outliers start: 25 outliers final: 10 residues processed: 200 average time/residue: 0.3614 time to fit residues: 112.8085 Evaluate side-chains 184 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 986 VAL Chi-restraints excluded: chain C residue 993 ASN Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain P residue 29 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 181 optimal weight: 4.9990 chunk 237 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 143 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.094103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.063345 restraints weight = 42739.502| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 2.70 r_work: 0.2567 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22428 Z= 0.183 Angle : 0.504 13.815 30442 Z= 0.256 Chirality : 0.040 0.155 3342 Planarity : 0.004 0.047 4015 Dihedral : 3.709 40.449 3018 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.15 % Allowed : 8.70 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.16), residues: 2736 helix: 2.33 (0.13), residues: 1466 sheet: 1.17 (0.33), residues: 226 loop : -0.20 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 616 HIS 0.003 0.001 HIS C 185 PHE 0.016 0.001 PHE C 193 TYR 0.026 0.001 TYR B1111 ARG 0.009 0.000 ARG Q 25 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 1131) hydrogen bonds : angle 4.01817 ( 3324) covalent geometry : bond 0.00443 (22428) covalent geometry : angle 0.50412 (30442) *********************** 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 204 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.8723 (mtpp) cc_final: 0.8415 (ptpp) REVERT: B 321 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8880 (pp) REVERT: B 541 MET cc_start: 0.9080 (mtp) cc_final: 0.8760 (mtp) REVERT: B 902 ARG cc_start: 0.8990 (ptt180) cc_final: 0.8625 (ptt-90) REVERT: B 1021 MET cc_start: 0.9157 (ttm) cc_final: 0.8944 (ttp) REVERT: B 1102 MET cc_start: 0.8993 (mmm) cc_final: 0.8734 (mtp) REVERT: C 14 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7919 (tm-30) REVERT: C 266 ARG cc_start: 0.8052 (ptm160) cc_final: 0.7445 (ttt90) REVERT: C 281 GLU cc_start: 0.8283 (mp0) cc_final: 0.7920 (mp0) REVERT: C 288 ASN cc_start: 0.7718 (t0) cc_final: 0.7464 (m-40) REVERT: C 667 MET cc_start: 0.9489 (mmt) cc_final: 0.9156 (mmt) REVERT: C 962 ASP cc_start: 0.8587 (t0) cc_final: 0.8133 (t0) REVERT: D 168 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8219 (p) REVERT: D 184 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7836 (mm) REVERT: D 218 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6612 (mmmt) REVERT: P 31 LYS cc_start: 0.8882 (mmtm) cc_final: 0.8628 (mmtm) REVERT: P 33 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8436 (tm-30) REVERT: P 36 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8811 (pt0) REVERT: P 39 GLU cc_start: 0.8990 (tp30) cc_final: 0.8732 (tm-30) REVERT: Q 24 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8285 (mt-10) outliers start: 27 outliers final: 17 residues processed: 196 average time/residue: 0.4120 time to fit residues: 125.3801 Evaluate side-chains 185 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 957 SER 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 557 ILE 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 58 LEU Chi-restraints excluded: chain D residue 168 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 30 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 83 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 239 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.093928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.064456 restraints weight = 42014.841| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.57 r_work: 0.2582 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22428 Z= 0.153 Angle : 0.489 14.234 30442 Z= 0.247 Chirality : 0.039 0.148 3342 Planarity : 0.004 0.050 4015 Dihedral : 3.648 38.190 3018 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.19 % Allowed : 8.74 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.16), residues: 2736 helix: 2.42 (0.13), residues: 1475 sheet: 1.21 (0.33), residues: 226 loop : -0.17 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 616 HIS 0.003 0.001 HIS C 185 PHE 0.025 0.001 PHE B 31 TYR 0.025 0.001 TYR B1111 ARG 0.011 0.000 ARG Q 25 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 1131) hydrogen bonds : angle 3.92264 ( 3324) covalent geometry : bond 0.00366 (22428) covalent geometry : angle 0.48883 (30442) *********************** 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 202 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.9086 (mmm) cc_final: 0.8536 (tpp) REVERT: B 264 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8442 (ptpp) REVERT: B 293 PHE cc_start: 0.8111 (t80) cc_final: 0.7865 (t80) REVERT: B 321 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8926 (pp) REVERT: B 541 MET cc_start: 0.9271 (mtp) cc_final: 0.8956 (mtp) REVERT: B 902 ARG cc_start: 0.9121 (ptt180) cc_final: 0.8774 (ptt-90) REVERT: B 1102 MET cc_start: 0.9117 (mmm) cc_final: 0.8872 (mtp) REVERT: C 14 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8090 (tm-30) REVERT: C 266 ARG cc_start: 0.8111 (ptm160) cc_final: 0.7516 (ttt90) REVERT: C 281 GLU cc_start: 0.8369 (mp0) cc_final: 0.7988 (mp0) REVERT: C 288 ASN cc_start: 0.7759 (t0) cc_final: 0.7489 (m-40) REVERT: C 667 MET cc_start: 0.9581 (mmt) cc_final: 0.9321 (mmt) REVERT: C 962 ASP cc_start: 0.8770 (t0) cc_final: 0.8327 (t0) REVERT: D 168 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.8130 (p) REVERT: D 218 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6718 (mmmt) REVERT: P 31 LYS cc_start: 0.8951 (mmtm) cc_final: 0.8601 (mmtm) REVERT: P 33 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8232 (tm-30) REVERT: P 39 GLU cc_start: 0.9019 (tp30) cc_final: 0.8763 (tm-30) REVERT: Q 3 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7741 (mmm160) REVERT: Q 24 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8318 (mt-10) REVERT: Q 30 LEU cc_start: 0.8522 (mm) cc_final: 0.8299 (mt) outliers start: 28 outliers final: 16 residues processed: 196 average time/residue: 0.3818 time to fit residues: 115.8883 Evaluate side-chains 188 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 699 THR 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 568 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 58 LEU Chi-restraints excluded: chain D residue 168 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 124 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 202 optimal weight: 8.9990 chunk 227 optimal weight: 8.9990 chunk 230 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 250 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.093130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.062485 restraints weight = 42779.653| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.65 r_work: 0.2562 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 22428 Z= 0.237 Angle : 0.544 13.865 30442 Z= 0.276 Chirality : 0.041 0.149 3342 Planarity : 0.004 0.053 4015 Dihedral : 3.828 39.480 3018 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.19 % Allowed : 8.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.16), residues: 2736 helix: 2.31 (0.13), residues: 1466 sheet: 1.20 (0.33), residues: 226 loop : -0.25 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 265 HIS 0.004 0.001 HIS C 843 PHE 0.020 0.002 PHE B 31 TYR 0.027 0.002 TYR B1111 ARG 0.010 0.000 ARG Q 25 Details of bonding type rmsd hydrogen bonds : bond 0.05105 ( 1131) hydrogen bonds : angle 4.11741 ( 3324) covalent geometry : bond 0.00571 (22428) covalent geometry : angle 0.54371 (30442) *********************** 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 : 6.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.8687 (mtpp) cc_final: 0.8344 (ptpp) REVERT: B 321 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8946 (pp) REVERT: B 541 MET cc_start: 0.9304 (mtp) cc_final: 0.8833 (mtp) REVERT: B 902 ARG cc_start: 0.9143 (ptt180) cc_final: 0.8798 (ptt-90) REVERT: B 1102 MET cc_start: 0.9130 (mmm) cc_final: 0.8853 (mtp) REVERT: C 14 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8455 (tm-30) REVERT: C 266 ARG cc_start: 0.8107 (ptm160) cc_final: 0.7529 (ttt90) REVERT: C 281 GLU cc_start: 0.8414 (mp0) cc_final: 0.8064 (mp0) REVERT: C 288 ASN cc_start: 0.7757 (t0) cc_final: 0.7442 (m-40) REVERT: C 962 ASP cc_start: 0.8880 (t0) cc_final: 0.8475 (t0) REVERT: D 160 VAL cc_start: 0.8140 (t) cc_final: 0.7913 (p) REVERT: D 218 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6771 (mmmt) REVERT: D 235 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7559 (tm-30) REVERT: P 31 LYS cc_start: 0.8972 (mmtm) cc_final: 0.8685 (mmtm) REVERT: P 33 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8372 (tm-30) REVERT: P 36 GLU cc_start: 0.9230 (tm-30) cc_final: 0.8965 (pt0) REVERT: Q 3 ARG cc_start: 0.8232 (mmm160) cc_final: 0.7940 (mmm160) REVERT: Q 24 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8342 (mt-10) outliers start: 28 outliers final: 19 residues processed: 199 average time/residue: 0.5400 time to fit residues: 172.3668 Evaluate side-chains 192 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 3.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 385 GLU Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 568 LEU 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 993 ASN Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 168 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 147 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 522 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.095464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.065206 restraints weight = 42395.346| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.64 r_work: 0.2622 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 22428 Z= 0.109 Angle : 0.473 14.316 30442 Z= 0.239 Chirality : 0.038 0.224 3342 Planarity : 0.004 0.052 4015 Dihedral : 3.605 36.485 3018 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.94 % Allowed : 9.25 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.16), residues: 2736 helix: 2.52 (0.14), residues: 1466 sheet: 1.13 (0.34), residues: 231 loop : -0.12 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 265 HIS 0.002 0.000 HIS C 185 PHE 0.021 0.001 PHE B 31 TYR 0.024 0.001 TYR B1111 ARG 0.011 0.000 ARG Q 25 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 1131) hydrogen bonds : angle 3.84491 ( 3324) covalent geometry : bond 0.00250 (22428) covalent geometry : angle 0.47337 (30442) *********************** 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 202 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 293 PHE cc_start: 0.8031 (t80) cc_final: 0.7830 (t80) REVERT: B 321 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8958 (pp) REVERT: B 541 MET cc_start: 0.9247 (mtp) cc_final: 0.8927 (mtp) REVERT: B 902 ARG cc_start: 0.9110 (ptt180) cc_final: 0.8770 (ptt-90) REVERT: B 1102 MET cc_start: 0.9084 (mmm) cc_final: 0.8379 (mtp) REVERT: C 14 GLU cc_start: 0.8614 (tm-30) cc_final: 0.7879 (tm-30) REVERT: C 253 ASP cc_start: 0.8372 (t0) cc_final: 0.7256 (t0) REVERT: C 266 ARG cc_start: 0.8120 (ptm160) cc_final: 0.7505 (ttt90) REVERT: C 281 GLU cc_start: 0.8431 (mp0) cc_final: 0.8133 (mp0) REVERT: C 288 ASN cc_start: 0.7771 (t0) cc_final: 0.7512 (m-40) REVERT: C 962 ASP cc_start: 0.8819 (t0) cc_final: 0.8394 (t0) REVERT: D 160 VAL cc_start: 0.8115 (t) cc_final: 0.7880 (p) REVERT: D 218 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6715 (mmmt) REVERT: D 235 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7548 (tm-30) REVERT: P 31 LYS cc_start: 0.9031 (mmtm) cc_final: 0.8681 (mmtm) REVERT: Q 3 ARG cc_start: 0.8176 (mmm160) cc_final: 0.7922 (mmm160) REVERT: Q 24 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8524 (mt-10) outliers start: 22 outliers final: 14 residues processed: 196 average time/residue: 0.3829 time to fit residues: 115.4855 Evaluate side-chains 188 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 3.051 ------------------------------------------------------------------------------- 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 657 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain C residue 115 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 5 LEU 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 170 optimal weight: 5.9990 chunk 20 optimal weight: 0.0030 chunk 249 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 229 optimal weight: 0.0270 chunk 72 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.6054 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.095404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.065165 restraints weight = 42222.278| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.63 r_work: 0.2624 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.3487 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= 0.120 Angle : 0.481 15.124 30442 Z= 0.241 Chirality : 0.038 0.170 3342 Planarity : 0.004 0.060 4015 Dihedral : 3.532 33.336 3018 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.85 % Allowed : 9.64 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.16), residues: 2736 helix: 2.55 (0.14), residues: 1467 sheet: 1.28 (0.34), residues: 229 loop : -0.10 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 265 HIS 0.003 0.001 HIS C 185 PHE 0.020 0.001 PHE B 31 TYR 0.024 0.001 TYR B1111 ARG 0.013 0.000 ARG Q 25 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 1131) hydrogen bonds : angle 3.81389 ( 3324) covalent geometry : bond 0.00282 (22428) covalent geometry : angle 0.48107 (30442) *********************** 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 195 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8953 (pp) REVERT: B 541 MET cc_start: 0.9254 (mtp) cc_final: 0.8898 (mtp) REVERT: B 902 ARG cc_start: 0.9105 (ptt180) cc_final: 0.8770 (ptt-90) REVERT: B 1102 MET cc_start: 0.9079 (mmm) cc_final: 0.8397 (mtp) REVERT: C 14 GLU cc_start: 0.8592 (tm-30) cc_final: 0.7851 (tm-30) REVERT: C 266 ARG cc_start: 0.8133 (ptm160) cc_final: 0.7512 (ttt90) REVERT: C 281 GLU cc_start: 0.8435 (mp0) cc_final: 0.8140 (mp0) REVERT: C 288 ASN cc_start: 0.7767 (t0) cc_final: 0.7525 (m-40) REVERT: C 962 ASP cc_start: 0.8819 (t0) cc_final: 0.8378 (t0) REVERT: C 1017 LEU cc_start: 0.9374 (mt) cc_final: 0.9165 (mt) REVERT: D 218 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6731 (mmmt) REVERT: D 235 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7597 (tm-30) REVERT: P 31 LYS cc_start: 0.9065 (mmtm) cc_final: 0.8739 (mmtm) REVERT: Q 24 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8654 (mt-10) outliers start: 20 outliers final: 14 residues processed: 191 average time/residue: 0.3564 time to fit residues: 105.9770 Evaluate side-chains 185 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 2.609 ------------------------------------------------------------------------------- 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 657 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain C residue 115 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 5 LEU 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: 8.9990 chunk 164 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 242 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** 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 = 0.094862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.065416 restraints weight = 42055.754| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.59 r_work: 0.2609 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2463 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22428 Z= 0.107 Angle : 0.470 13.545 30442 Z= 0.236 Chirality : 0.037 0.173 3342 Planarity : 0.004 0.063 4015 Dihedral : 3.454 31.344 3018 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.77 % Allowed : 9.98 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.16), residues: 2736 helix: 2.64 (0.14), residues: 1461 sheet: 1.35 (0.35), residues: 229 loop : -0.03 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q 13 HIS 0.003 0.000 HIS C 185 PHE 0.020 0.001 PHE B 31 TYR 0.023 0.001 TYR B1111 ARG 0.015 0.000 ARG Q 25 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 1131) hydrogen bonds : angle 3.74254 ( 3324) covalent geometry : bond 0.00248 (22428) covalent geometry : angle 0.46956 (30442) ********************** 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 194 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 321 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8940 (pp) REVERT: B 541 MET cc_start: 0.9248 (mtp) cc_final: 0.8924 (mtp) REVERT: B 902 ARG cc_start: 0.9090 (ptt180) cc_final: 0.8735 (ptt-90) REVERT: B 1102 MET cc_start: 0.9090 (mmm) cc_final: 0.8446 (mtp) REVERT: C 266 ARG cc_start: 0.8108 (ptm160) cc_final: 0.7493 (ttt90) REVERT: C 281 GLU cc_start: 0.8439 (mp0) cc_final: 0.8134 (mp0) REVERT: C 288 ASN cc_start: 0.7746 (t0) cc_final: 0.7481 (m-40) REVERT: C 962 ASP cc_start: 0.8774 (t0) cc_final: 0.8333 (t0) REVERT: D 218 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6726 (mmmt) REVERT: D 235 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7587 (tm-30) REVERT: P 31 LYS cc_start: 0.9077 (mmtm) cc_final: 0.8769 (mmtm) REVERT: P 33 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8103 (tm-30) REVERT: Q 24 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8499 (mt-10) outliers start: 18 outliers final: 15 residues processed: 190 average time/residue: 0.5397 time to fit residues: 160.0768 Evaluate side-chains 186 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 3.642 ------------------------------------------------------------------------------- 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 657 VAL Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 117 ASP 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 5 LEU 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 9 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 235 optimal weight: 20.0000 chunk 196 optimal weight: 0.9990 chunk 238 optimal weight: 0.0770 chunk 237 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 247 optimal weight: 8.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- 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 = 0.3329 r_free = 0.3329 target = 0.095237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.065841 restraints weight = 41997.567| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.59 r_work: 0.2628 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22428 Z= 0.103 Angle : 0.473 13.993 30442 Z= 0.237 Chirality : 0.037 0.165 3342 Planarity : 0.004 0.056 4015 Dihedral : 3.407 31.730 3018 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.81 % Allowed : 10.15 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.16), residues: 2736 helix: 2.66 (0.14), residues: 1465 sheet: 1.32 (0.34), residues: 235 loop : -0.01 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q 13 HIS 0.002 0.000 HIS C 185 PHE 0.019 0.001 PHE B 31 TYR 0.023 0.001 TYR B1111 ARG 0.014 0.000 ARG Q 25 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 1131) hydrogen bonds : angle 3.70789 ( 3324) covalent geometry : bond 0.00238 (22428) covalent geometry : angle 0.47271 (30442) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11552.96 seconds wall clock time: 207 minutes 11.98 seconds (12431.98 seconds total)