Starting phenix.real_space_refine on Mon Aug 25 00:21:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5mbv_3460/08_2025/5mbv_3460.cif Found real_map, /net/cci-nas-00/data/ceres_data/5mbv_3460/08_2025/5mbv_3460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5mbv_3460/08_2025/5mbv_3460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5mbv_3460/08_2025/5mbv_3460.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5mbv_3460/08_2025/5mbv_3460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5mbv_3460/08_2025/5mbv_3460.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 15225 2.51 5 N 4267 2.21 5 O 4516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 137 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24118 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 9037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1127, 9037 Classifications: {'peptide': 1127} Link IDs: {'PTRANS': 50, 'TRANS': 1076} Chain breaks: 2 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: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4570 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 24, 'TRANS': 568} Chain breaks: 2 Chain: "A" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 817 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain: "E" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 616 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Time building chain proxies: 5.86, per 1000 atoms: 0.24 Number of scatterers: 24118 At special positions: 0 Unit cell: (152.76, 160.8, 116.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 4516 8.00 N 4267 7.00 C 15225 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: 2.50 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.4 microseconds 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5700 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 17 sheets defined 58.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.672A pdb=" N ALA B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 55 through 58 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 128 through 138 removed outlier: 3.627A pdb=" N GLN B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 4.055A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 171 Processing helix chain 'B' and resid 176 through 187 removed outlier: 3.904A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 5.037A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 240 removed outlier: 3.805A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 4.178A pdb=" N ASN B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 280 Processing helix chain 'B' and resid 281 through 289 Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.889A pdb=" N ASP B 314 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU B 319 " --> pdb=" O GLN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 3.673A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.525A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 removed outlier: 3.809A pdb=" N LEU B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.785A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 424 removed outlier: 4.400A pdb=" N PHE B 422 " --> pdb=" O ILE B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.670A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 510 through 534 Processing helix chain 'B' and resid 560 through 574 removed outlier: 3.702A pdb=" N LEU B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.623A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 597 " --> pdb=" O ALA B 593 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP B 598 " --> pdb=" O GLN B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 Processing helix chain 'B' and resid 624 through 634 Processing helix chain 'B' and resid 634 through 655 removed outlier: 3.632A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 669 removed outlier: 3.573A 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 701 removed outlier: 3.779A pdb=" N ARG B 683 " --> pdb=" O GLY B 679 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 717 removed outlier: 3.520A pdb=" N GLU B 717 " --> pdb=" O GLN B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 731 through 735 Processing helix chain 'B' and resid 783 through 808 removed outlier: 3.788A pdb=" N VAL B 787 " --> pdb=" O ALA B 783 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 827 removed outlier: 4.158A pdb=" N LYS B 827 " --> pdb=" O ARG B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 835 removed outlier: 4.366A pdb=" N HIS B 834 " --> pdb=" O THR B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 843 removed outlier: 3.507A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.959A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 941 through 945 removed outlier: 3.534A pdb=" N PHE B 945 " --> pdb=" O PRO B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 962 removed outlier: 3.849A pdb=" N PHE B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) removed outlier: 3.843A 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 986 through 999 removed outlier: 4.308A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 995 " --> pdb=" O THR B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 Processing helix chain 'B' and resid 1013 through 1015 No H-bonds generated for 'chain 'B' and resid 1013 through 1015' Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.625A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1048 Processing helix chain 'B' and resid 1094 through 1105 removed outlier: 3.635A pdb=" N ALA B1099 " --> pdb=" O GLN B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1106 through 1126 removed outlier: 4.123A 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 1163 through 1174 removed outlier: 3.572A pdb=" N LEU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.948A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 55 removed outlier: 3.813A pdb=" N ALA C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 77 removed outlier: 3.577A pdb=" N ARG C 75 " --> pdb=" O ASP C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 102 removed outlier: 3.677A pdb=" N TRP C 93 " --> pdb=" O GLN C 89 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 116 removed outlier: 3.653A pdb=" N HIS C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TYR C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.751A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 removed outlier: 3.890A pdb=" N GLN C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 166 " --> pdb=" O GLN C 162 " (cutoff:3.500A) Proline residue: C 167 - end of helix Processing helix chain 'C' and resid 185 through 199 removed outlier: 3.988A pdb=" N TYR C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 Processing helix chain 'C' and resid 255 through 262 removed outlier: 3.637A pdb=" N ALA C 258 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 261 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR C 262 " --> pdb=" O LYS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 removed outlier: 4.137A pdb=" N ASN C 282 " --> pdb=" O ARG C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 315 removed outlier: 4.065A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.988A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.555A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP C 400 " --> pdb=" O MET C 396 " (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 removed outlier: 3.693A pdb=" N TYR C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Proline residue: C 420 - end of helix Processing helix chain 'C' and resid 447 through 458 removed outlier: 3.621A pdb=" N LEU C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 463 Processing helix chain 'C' and resid 466 through 474 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.805A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.787A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.646A pdb=" N VAL C 511 " --> pdb=" O ASP C 507 " (cutoff:3.500A) 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 578 removed outlier: 3.646A pdb=" N GLY C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 586 Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.168A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 597 " --> pdb=" O ASP C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 626 removed outlier: 4.389A pdb=" N ALA C 608 " --> pdb=" O GLU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 647 removed outlier: 3.879A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C 647 " --> pdb=" O GLN C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 removed outlier: 3.690A 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 795 removed outlier: 3.513A pdb=" N GLN C 795 " --> pdb=" O GLN C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 806 through 812 Processing helix chain 'C' and resid 834 through 843 removed outlier: 4.112A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 851 removed outlier: 3.675A pdb=" N PHE C 849 " --> pdb=" O VAL C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 890 removed outlier: 3.581A pdb=" N ILE C 880 " --> pdb=" O SER C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 904 removed outlier: 4.007A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 935 removed outlier: 3.571A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN C 926 " --> pdb=" O GLN C 922 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 933 " --> pdb=" O ASP C 929 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N CYS C 934 " --> pdb=" O ARG C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 990 removed outlier: 4.004A pdb=" N SER C 990 " --> pdb=" O VAL C 986 " (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 1076 Processing helix chain 'C' and resid 1087 through 1094 removed outlier: 4.001A pdb=" N LEU C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP C1094 " --> pdb=" O TYR C1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1113 through 1120 removed outlier: 3.969A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.539A pdb=" N GLU D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU D 12 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 65 through 71 Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.688A pdb=" N CYS D 84 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (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: 3.713A 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 232 Processing helix chain 'D' and resid 240 through 245 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.759A pdb=" N ASP D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.602A 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: 3.919A pdb=" N ASN D 318 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 334 removed outlier: 3.571A pdb=" N ARG D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 351 removed outlier: 3.586A pdb=" N SER D 351 " --> pdb=" O SER D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 375 removed outlier: 3.999A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.615A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 415 through 424 Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.696A pdb=" N ASN D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 removed outlier: 3.883A pdb=" N GLU D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.789A pdb=" N LEU D 527 " --> pdb=" O PRO D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 571 Processing helix chain 'D' and resid 582 through 592 Processing helix chain 'D' and resid 599 through 605 removed outlier: 3.547A pdb=" N SER D 605 " --> pdb=" O ALA D 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 77 removed outlier: 3.612A pdb=" N ALA A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 4.073A pdb=" N PHE A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.663A pdb=" N GLN A 113 " --> pdb=" O ASP A 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 79 removed outlier: 3.791A pdb=" N LYS E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY E 78 " --> pdb=" O ASP E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 93 removed outlier: 3.719A pdb=" N PHE E 84 " --> pdb=" O PRO E 80 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN E 93 " --> pdb=" O ILE E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 107 Processing helix chain 'E' and resid 109 through 135 removed outlier: 3.621A pdb=" N GLN E 113 " --> pdb=" O ASP E 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.602A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 207 through 208 Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA4, first strand: chain 'B' and resid 487 through 490 Processing sheet with id=AA5, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.331A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS B 812 " --> pdb=" O PRO B 750 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS B 500 " --> pdb=" O LEU B 815 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL B 817 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N TRP B 502 " --> pdb=" O VAL B 817 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA B 870 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU B 503 " --> pdb=" O ALA B 870 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 904 through 905 removed outlier: 6.578A pdb=" N VAL B1058 " --> pdb=" O GLU B1029 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU B1029 " --> pdb=" O VAL B1058 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B1064 " --> pdb=" O PHE B1023 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B1023 " --> pdb=" O GLY B1064 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B1068 " --> pdb=" O VAL B1019 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B1019 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE B1070 " --> pdb=" O LYS B1017 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LYS B1017 " --> pdb=" O PHE B1070 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 904 through 905 removed outlier: 9.735A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B1070 " --> pdb=" O TYR B1077 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N TYR B1076 " --> pdb=" O GLY B1137 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ILE B1139 " --> pdb=" O TYR B1076 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU B1078 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU B1141 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASP B1080 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 61 removed outlier: 4.457A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N THR C 241 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL C 4 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ALA C 325 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N HIS C 6 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ARG C 265 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.282A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 437 through 439 removed outlier: 6.390A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR C 375 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N TYR C 731 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N HIS C 377 " --> pdb=" O TYR C 731 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 831 through 833 removed outlier: 3.689A pdb=" N THR C 953 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 831 through 833 removed outlier: 3.689A pdb=" N THR C 953 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 14.975A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 12.527A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1050 through 1051 removed outlier: 3.528A pdb=" N ALA C1056 " --> pdb=" O ASP C1051 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.126A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 237 through 239 removed outlier: 9.507A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU D 201 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY D 296 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 395 through 396 removed outlier: 6.078A pdb=" N ALA D 549 " --> pdb=" O SER D 578 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N TYR D 580 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU D 551 " --> pdb=" O TYR D 580 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN D 439 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE D 552 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU D 441 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 519 through 522 removed outlier: 5.299A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 480 " --> pdb=" O ALA D 501 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET D 483 " --> pdb=" O GLU D 531 " (cutoff:3.500A) 1178 hydrogen bonds defined for protein. 3396 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: 6.03 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8254 1.34 - 1.46: 5194 1.46 - 1.58: 11005 1.58 - 1.69: 0 1.69 - 1.81: 185 Bond restraints: 24638 Sorted by residual: bond pdb=" N ALA C 161 " pdb=" CA ALA C 161 " ideal model delta sigma weight residual 1.456 1.470 -0.014 1.23e-02 6.61e+03 1.35e+00 bond pdb=" C ARG C 968 " pdb=" N PRO C 969 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.32e+00 bond pdb=" CG PRO D 428 " pdb=" CD PRO D 428 " ideal model delta sigma weight residual 1.503 1.464 0.039 3.40e-02 8.65e+02 1.29e+00 bond pdb=" N GLY C 555 " pdb=" CA GLY C 555 " ideal model delta sigma weight residual 1.438 1.451 -0.013 1.41e-02 5.03e+03 8.17e-01 bond pdb=" C SER D 64 " pdb=" N HIS D 65 " ideal model delta sigma weight residual 1.331 1.349 -0.018 2.07e-02 2.33e+03 7.76e-01 ... (remaining 24633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 33134 2.16 - 4.33: 252 4.33 - 6.49: 22 6.49 - 8.66: 2 8.66 - 10.82: 1 Bond angle restraints: 33411 Sorted by residual: angle pdb=" C ASP B 882 " pdb=" CA ASP B 882 " pdb=" CB ASP B 882 " ideal model delta sigma weight residual 116.34 110.36 5.98 1.40e+00 5.10e-01 1.83e+01 angle pdb=" C ASP D 389 " pdb=" N PHE D 390 " pdb=" CA PHE D 390 " ideal model delta sigma weight residual 121.54 128.24 -6.70 1.91e+00 2.74e-01 1.23e+01 angle pdb=" N GLY C 555 " pdb=" CA GLY C 555 " pdb=" C GLY C 555 " ideal model delta sigma weight residual 112.79 116.64 -3.85 1.20e+00 6.94e-01 1.03e+01 angle pdb=" C GLY D 479 " pdb=" N ARG D 480 " pdb=" CA ARG D 480 " ideal model delta sigma weight residual 121.27 110.45 10.82 3.40e+00 8.65e-02 1.01e+01 angle pdb=" C PHE D 390 " pdb=" N THR D 391 " pdb=" CA THR D 391 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.47e+00 ... (remaining 33406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 14233 17.76 - 35.51: 566 35.51 - 53.27: 87 53.27 - 71.02: 18 71.02 - 88.78: 15 Dihedral angle restraints: 14919 sinusoidal: 6135 harmonic: 8784 Sorted by residual: dihedral pdb=" CA GLN C 545 " pdb=" C GLN C 545 " pdb=" N SER C 546 " pdb=" CA SER C 546 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ALA C 283 " pdb=" C ALA C 283 " pdb=" N GLY C 284 " pdb=" CA GLY C 284 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA GLY C 657 " pdb=" C GLY C 657 " pdb=" N PRO C 658 " pdb=" CA PRO C 658 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 14916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2452 0.028 - 0.055: 775 0.055 - 0.083: 232 0.083 - 0.111: 156 0.111 - 0.139: 42 Chirality restraints: 3657 Sorted by residual: chirality pdb=" CA ILE C 864 " pdb=" N ILE C 864 " pdb=" C ILE C 864 " pdb=" CB ILE C 864 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE C 661 " pdb=" N ILE C 661 " pdb=" C ILE C 661 " pdb=" CB ILE C 661 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA VAL B 126 " pdb=" N VAL B 126 " pdb=" C VAL B 126 " pdb=" CB VAL B 126 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 3654 not shown) Planarity restraints: 4403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO C 658 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 907 " -0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO C 908 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 908 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 908 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 381 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO C 382 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 382 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 382 " -0.026 5.00e-02 4.00e+02 ... (remaining 4400 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 652 2.72 - 3.26: 24369 3.26 - 3.81: 36975 3.81 - 4.35: 47811 4.35 - 4.90: 79038 Nonbonded interactions: 188845 Sorted by model distance: nonbonded pdb=" O LEU D 67 " pdb=" OG1 THR D 70 " model vdw 2.172 3.040 nonbonded pdb=" OH TYR D 316 " pdb=" O ALA D 601 " model vdw 2.221 3.040 nonbonded pdb=" O TYR B 580 " pdb=" ND2 ASN B 583 " model vdw 2.221 3.120 nonbonded pdb=" O ARG B 255 " pdb=" OH TYR B 280 " model vdw 2.227 3.040 nonbonded pdb=" O GLU B 978 " pdb=" NE2 GLN C 617 " model vdw 2.256 3.120 ... (remaining 188840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.680 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 : 0.002 0.039 24638 Z= 0.099 Angle : 0.506 10.823 33411 Z= 0.308 Chirality : 0.036 0.139 3657 Planarity : 0.003 0.069 4403 Dihedral : 10.209 88.779 9219 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.74 % Favored : 95.16 % Rotamer: Outliers : 0.74 % Allowed : 3.82 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.37 (0.12), residues: 2996 helix: -3.28 (0.08), residues: 1534 sheet: -0.33 (0.27), residues: 290 loop : -0.86 (0.16), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 572 TYR 0.010 0.001 TYR D 477 PHE 0.007 0.001 PHE C 694 TRP 0.010 0.001 TRP C 248 HIS 0.003 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.00174 (24638) covalent geometry : angle 0.50627 (33411) hydrogen bonds : bond 0.25537 ( 1175) hydrogen bonds : angle 8.63392 ( 3396) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 278 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 259 ARG cc_start: 0.9414 (ttp80) cc_final: 0.9154 (ttt180) REVERT: B 311 GLU cc_start: 0.9335 (tt0) cc_final: 0.9018 (tp30) REVERT: B 314 ASP cc_start: 0.9055 (t0) cc_final: 0.8827 (t0) REVERT: B 660 MET cc_start: 0.8351 (ttp) cc_final: 0.7737 (tmm) REVERT: B 906 TYR cc_start: 0.7780 (p90) cc_final: 0.7559 (t80) REVERT: B 992 GLU cc_start: 0.9028 (pt0) cc_final: 0.8439 (mp0) REVERT: B 1015 ARG cc_start: 0.8365 (mmt90) cc_final: 0.8141 (tmm-80) REVERT: B 1050 CYS cc_start: 0.8658 (m) cc_final: 0.8423 (m) REVERT: B 1056 MET cc_start: 0.7680 (mtp) cc_final: 0.7431 (mpp) REVERT: B 1058 VAL cc_start: 0.7068 (t) cc_final: 0.6807 (m) REVERT: B 1069 VAL cc_start: 0.6350 (OUTLIER) cc_final: 0.5983 (p) REVERT: B 1077 TYR cc_start: 0.8194 (m-80) cc_final: 0.7053 (m-80) REVERT: B 1113 LEU cc_start: 0.7829 (mt) cc_final: 0.7348 (pp) REVERT: C 272 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.8013 (ttp80) REVERT: C 350 VAL cc_start: 0.8872 (t) cc_final: 0.8573 (m) REVERT: C 634 LEU cc_start: 0.8828 (tp) cc_final: 0.8608 (tp) REVERT: C 944 ASP cc_start: 0.7486 (t0) cc_final: 0.7260 (m-30) REVERT: C 1080 MET cc_start: 0.8743 (tpp) cc_final: 0.8535 (ptp) REVERT: D 226 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8112 (m) REVERT: D 242 ARG cc_start: 0.9235 (ttt-90) cc_final: 0.8992 (tpp-160) REVERT: D 273 MET cc_start: 0.8787 (mtm) cc_final: 0.7974 (mpp) REVERT: D 278 MET cc_start: 0.9023 (mmm) cc_final: 0.8750 (mmm) REVERT: D 295 LEU cc_start: 0.8514 (mt) cc_final: 0.7976 (tt) REVERT: D 547 ASP cc_start: 0.8848 (t0) cc_final: 0.8612 (t70) REVERT: A 100 LYS cc_start: 0.9556 (mtmt) cc_final: 0.9333 (tptt) REVERT: A 115 ARG cc_start: 0.9170 (mmm160) cc_final: 0.8823 (mmm160) REVERT: A 116 MET cc_start: 0.9254 (tpt) cc_final: 0.8956 (mmm) REVERT: E 111 GLU cc_start: 0.9639 (tt0) cc_final: 0.9192 (tp30) REVERT: E 122 TYR cc_start: 0.9162 (t80) cc_final: 0.8803 (t80) REVERT: E 123 MET cc_start: 0.9555 (mtp) cc_final: 0.9242 (mtp) REVERT: E 127 ILE cc_start: 0.9425 (mt) cc_final: 0.9146 (tp) outliers start: 19 outliers final: 1 residues processed: 293 average time/residue: 0.1994 time to fit residues: 88.1186 Evaluate side-chains 146 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 1069 VAL Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 6.9990 overall best weight: 4.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN B 463 GLN B 484 ASN B 650 GLN B 765 GLN B 894 GLN B1134 HIS C 126 GLN C 228 GLN C 233 HIS C 336 HIS C 390 HIS C 448 HIS C 510 ASN C 647 GLN C 660 ASN C 737 GLN C 759 HIS C 817 HIS C 881 ASN C 886 ASN C 920 GLN C 925 GLN C 926 GLN C 951 GLN C 979 GLN C1108 GLN D 44 HIS D 79 GLN D 115 ASN D 255 HIS D 256 HIS A 113 GLN A 131 GLN E 81 GLN ** E 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 HIS E 131 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.061173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.046436 restraints weight = 131502.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.047611 restraints weight = 75323.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.048314 restraints weight = 51583.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.048811 restraints weight = 41171.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.049125 restraints weight = 35591.456| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24638 Z= 0.194 Angle : 0.616 7.551 33411 Z= 0.318 Chirality : 0.041 0.160 3657 Planarity : 0.004 0.061 4403 Dihedral : 4.262 45.432 3317 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.40 % Favored : 97.56 % Rotamer: Outliers : 1.13 % Allowed : 7.57 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.14), residues: 2996 helix: -0.43 (0.12), residues: 1559 sheet: -0.17 (0.26), residues: 293 loop : -0.62 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 649 TYR 0.021 0.002 TYR B1111 PHE 0.019 0.002 PHE B 945 TRP 0.015 0.001 TRP C 248 HIS 0.010 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00420 (24638) covalent geometry : angle 0.61612 (33411) hydrogen bonds : bond 0.04470 ( 1175) hydrogen bonds : angle 4.74941 ( 3396) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.8637 (pttp) cc_final: 0.8430 (pttm) REVERT: B 311 GLU cc_start: 0.8915 (tt0) cc_final: 0.8673 (tp30) REVERT: B 658 MET cc_start: 0.8748 (mmm) cc_final: 0.8237 (mmt) REVERT: B 660 MET cc_start: 0.8698 (ttp) cc_final: 0.8043 (tmm) REVERT: B 815 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8483 (pp) REVERT: B 1021 MET cc_start: 0.7115 (tmm) cc_final: 0.5197 (tmm) REVERT: B 1050 CYS cc_start: 0.8500 (m) cc_final: 0.8272 (m) REVERT: B 1056 MET cc_start: 0.7964 (mtp) cc_final: 0.7714 (mpp) REVERT: B 1061 MET cc_start: 0.7742 (mmm) cc_final: 0.7526 (mmm) REVERT: B 1070 PHE cc_start: 0.8988 (p90) cc_final: 0.8443 (p90) REVERT: B 1098 MET cc_start: 0.4527 (mmp) cc_final: 0.3635 (mpp) REVERT: C 34 MET cc_start: 0.7850 (mmm) cc_final: 0.7629 (tpp) REVERT: C 59 ASN cc_start: 0.7710 (m-40) cc_final: 0.7360 (t0) REVERT: C 96 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8616 (tpt) REVERT: C 680 MET cc_start: 0.9165 (mmm) cc_final: 0.8516 (mmt) REVERT: C 787 MET cc_start: 0.8321 (mpp) cc_final: 0.8010 (mpp) REVERT: C 1080 MET cc_start: 0.8121 (tpp) cc_final: 0.7816 (ptp) REVERT: C 1102 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8425 (ppp) REVERT: D 226 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.7921 (m) REVERT: D 295 LEU cc_start: 0.8674 (mt) cc_final: 0.8255 (tt) REVERT: E 116 MET cc_start: 0.8911 (tpp) cc_final: 0.8229 (mmm) REVERT: E 122 TYR cc_start: 0.8991 (t80) cc_final: 0.8536 (t80) outliers start: 29 outliers final: 10 residues processed: 182 average time/residue: 0.1777 time to fit residues: 51.0588 Evaluate side-chains 143 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 1102 MET Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain A residue 79 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 158 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 138 optimal weight: 20.0000 chunk 294 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 279 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN B 181 GLN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 944 GLN B1072 HIS ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN D 241 HIS E 119 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.059161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.044450 restraints weight = 133844.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.045583 restraints weight = 75822.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.046264 restraints weight = 52735.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.046699 restraints weight = 42452.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.046858 restraints weight = 37102.603| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24638 Z= 0.213 Angle : 0.615 9.522 33411 Z= 0.313 Chirality : 0.042 0.274 3657 Planarity : 0.004 0.054 4403 Dihedral : 4.346 46.525 3316 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.86 % Rotamer: Outliers : 1.52 % Allowed : 7.76 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.15), residues: 2996 helix: 0.84 (0.13), residues: 1563 sheet: 0.04 (0.29), residues: 276 loop : -0.65 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 242 TYR 0.022 0.002 TYR C 794 PHE 0.015 0.002 PHE C 421 TRP 0.014 0.001 TRP B1085 HIS 0.008 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00467 (24638) covalent geometry : angle 0.61461 (33411) hydrogen bonds : bond 0.04208 ( 1175) hydrogen bonds : angle 4.47342 ( 3396) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 658 MET cc_start: 0.8734 (mmm) cc_final: 0.8341 (mmt) REVERT: B 1015 ARG cc_start: 0.8601 (mmt90) cc_final: 0.8321 (tmm-80) REVERT: B 1021 MET cc_start: 0.7490 (tmm) cc_final: 0.6147 (tmm) REVERT: B 1050 CYS cc_start: 0.8507 (m) cc_final: 0.8294 (m) REVERT: B 1061 MET cc_start: 0.8263 (mmm) cc_final: 0.7549 (mmm) REVERT: B 1102 MET cc_start: 0.7845 (ppp) cc_final: 0.7644 (ppp) REVERT: C 34 MET cc_start: 0.8165 (mmm) cc_final: 0.7903 (tpp) REVERT: C 396 MET cc_start: 0.8612 (mpp) cc_final: 0.8395 (mpp) REVERT: C 397 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8907 (mm) REVERT: C 667 MET cc_start: 0.8536 (mmt) cc_final: 0.8240 (mmt) REVERT: C 680 MET cc_start: 0.9056 (mmm) cc_final: 0.8825 (mmt) REVERT: C 1102 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8636 (ppp) REVERT: D 226 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.7869 (m) REVERT: D 295 LEU cc_start: 0.8714 (mt) cc_final: 0.8450 (tp) REVERT: D 462 MET cc_start: 0.2322 (ppp) cc_final: 0.1917 (ppp) REVERT: D 483 MET cc_start: 0.6093 (ppp) cc_final: 0.5524 (ppp) REVERT: D 500 ILE cc_start: 0.7003 (OUTLIER) cc_final: 0.6796 (pt) REVERT: D 536 MET cc_start: 0.7147 (tpp) cc_final: 0.6857 (tpp) REVERT: A 116 MET cc_start: 0.8716 (mmm) cc_final: 0.8338 (mmm) REVERT: E 70 GLU cc_start: 0.8625 (pp20) cc_final: 0.8413 (tm-30) REVERT: E 122 TYR cc_start: 0.9012 (t80) cc_final: 0.8511 (t80) outliers start: 39 outliers final: 15 residues processed: 161 average time/residue: 0.1599 time to fit residues: 41.8272 Evaluate side-chains 139 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 882 ASP Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 537 MET Chi-restraints excluded: chain C residue 1102 MET Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 107 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 153 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 290 optimal weight: 5.9990 chunk 137 optimal weight: 0.0060 chunk 35 optimal weight: 7.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN B 202 GLN B 307 HIS B 834 HIS B 911 GLN C 185 HIS C 237 HIS C 793 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.059580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.044883 restraints weight = 132950.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.045998 restraints weight = 75030.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.046711 restraints weight = 51874.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.047174 restraints weight = 41322.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.047422 restraints weight = 36224.315| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24638 Z= 0.140 Angle : 0.528 7.201 33411 Z= 0.265 Chirality : 0.040 0.191 3657 Planarity : 0.003 0.049 4403 Dihedral : 4.109 44.071 3316 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.20 % Rotamer: Outliers : 1.56 % Allowed : 8.74 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.15), residues: 2996 helix: 1.42 (0.13), residues: 1551 sheet: 0.19 (0.29), residues: 275 loop : -0.60 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 668 TYR 0.021 0.001 TYR B1111 PHE 0.011 0.001 PHE B 351 TRP 0.010 0.001 TRP B1085 HIS 0.005 0.001 HIS E 91 Details of bonding type rmsd covalent geometry : bond 0.00307 (24638) covalent geometry : angle 0.52819 (33411) hydrogen bonds : bond 0.03476 ( 1175) hydrogen bonds : angle 4.15460 ( 3396) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 658 MET cc_start: 0.8651 (mmm) cc_final: 0.8348 (mmt) REVERT: B 665 MET cc_start: 0.8156 (mpp) cc_final: 0.7609 (mpp) REVERT: B 1015 ARG cc_start: 0.8586 (mmt90) cc_final: 0.8300 (tmm-80) REVERT: B 1021 MET cc_start: 0.7586 (tmm) cc_final: 0.6143 (tmm) REVERT: B 1061 MET cc_start: 0.8323 (mmm) cc_final: 0.7627 (mmm) REVERT: C 34 MET cc_start: 0.8111 (mmm) cc_final: 0.7804 (tpp) REVERT: C 96 MET cc_start: 0.9095 (mmm) cc_final: 0.8562 (mmm) REVERT: C 397 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8792 (mm) REVERT: C 680 MET cc_start: 0.9022 (mmm) cc_final: 0.8750 (mmm) REVERT: C 787 MET cc_start: 0.8455 (mpp) cc_final: 0.7913 (mpp) REVERT: C 1057 MET cc_start: 0.6717 (mtm) cc_final: 0.6409 (ttm) REVERT: C 1102 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8539 (ppp) REVERT: D 226 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8033 (m) REVERT: D 295 LEU cc_start: 0.8772 (mt) cc_final: 0.8451 (tt) REVERT: D 462 MET cc_start: 0.2425 (ppp) cc_final: 0.2103 (ppp) REVERT: D 483 MET cc_start: 0.6111 (ppp) cc_final: 0.5484 (ppp) REVERT: D 500 ILE cc_start: 0.7018 (OUTLIER) cc_final: 0.6776 (pt) REVERT: D 518 ASN cc_start: 0.7892 (m-40) cc_final: 0.7523 (t0) REVERT: D 536 MET cc_start: 0.7233 (tpp) cc_final: 0.6727 (tpt) REVERT: A 116 MET cc_start: 0.8650 (mmm) cc_final: 0.8366 (mmm) REVERT: E 116 MET cc_start: 0.8871 (tpp) cc_final: 0.8559 (mmm) REVERT: E 122 TYR cc_start: 0.8938 (t80) cc_final: 0.8444 (t80) outliers start: 40 outliers final: 17 residues processed: 158 average time/residue: 0.1542 time to fit residues: 40.2871 Evaluate side-chains 135 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 1102 MET Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 107 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 63 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 92 optimal weight: 30.0000 chunk 45 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 74 optimal weight: 0.0980 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 601 GLN C 850 GLN ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.058402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.043725 restraints weight = 133905.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.044855 restraints weight = 76827.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.045549 restraints weight = 52806.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.045981 restraints weight = 42146.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.046258 restraints weight = 37119.336| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24638 Z= 0.188 Angle : 0.580 9.902 33411 Z= 0.291 Chirality : 0.040 0.166 3657 Planarity : 0.004 0.048 4403 Dihedral : 4.196 43.365 3316 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Rotamer: Outliers : 1.76 % Allowed : 9.44 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.15), residues: 2996 helix: 1.54 (0.13), residues: 1553 sheet: 0.24 (0.30), residues: 270 loop : -0.51 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 115 TYR 0.016 0.001 TYR C 794 PHE 0.014 0.001 PHE C 901 TRP 0.013 0.001 TRP B1085 HIS 0.006 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00415 (24638) covalent geometry : angle 0.58039 (33411) hydrogen bonds : bond 0.03769 ( 1175) hydrogen bonds : angle 4.23807 ( 3396) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 504 MET cc_start: 0.8913 (tpp) cc_final: 0.8124 (tpp) REVERT: B 658 MET cc_start: 0.8768 (mmm) cc_final: 0.8521 (mmt) REVERT: B 660 MET cc_start: 0.8528 (ttp) cc_final: 0.7905 (ttp) REVERT: B 1021 MET cc_start: 0.7619 (tmm) cc_final: 0.5930 (tmm) REVERT: B 1061 MET cc_start: 0.8432 (mmm) cc_final: 0.7540 (mmm) REVERT: C 34 MET cc_start: 0.8196 (mmm) cc_final: 0.7908 (tpp) REVERT: C 397 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8823 (mm) REVERT: C 667 MET cc_start: 0.8528 (mmt) cc_final: 0.8177 (mmt) REVERT: C 680 MET cc_start: 0.9024 (mmm) cc_final: 0.8714 (mmm) REVERT: C 787 MET cc_start: 0.8250 (mpp) cc_final: 0.7610 (mpp) REVERT: C 1079 MET cc_start: 0.7434 (pmm) cc_final: 0.7112 (pmm) REVERT: C 1102 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8608 (ppp) REVERT: D 269 ASP cc_start: 0.8273 (t0) cc_final: 0.7934 (t0) REVERT: D 273 MET cc_start: 0.8203 (mpp) cc_final: 0.7255 (mpp) REVERT: D 295 LEU cc_start: 0.8758 (mt) cc_final: 0.8357 (tt) REVERT: D 462 MET cc_start: 0.2429 (ppp) cc_final: 0.2154 (ppp) REVERT: D 483 MET cc_start: 0.6369 (ppp) cc_final: 0.5909 (ppp) REVERT: D 518 ASN cc_start: 0.7786 (m-40) cc_final: 0.7508 (t0) REVERT: D 536 MET cc_start: 0.7337 (tpp) cc_final: 0.6877 (tpt) REVERT: A 116 MET cc_start: 0.8663 (mmm) cc_final: 0.8130 (mmm) REVERT: E 70 GLU cc_start: 0.8586 (pp20) cc_final: 0.8200 (tm-30) REVERT: E 75 MET cc_start: 0.9177 (mtt) cc_final: 0.8931 (mpp) REVERT: E 111 GLU cc_start: 0.8608 (pm20) cc_final: 0.8363 (pm20) REVERT: E 116 MET cc_start: 0.8974 (tpp) cc_final: 0.8329 (mmm) REVERT: E 122 TYR cc_start: 0.9060 (t80) cc_final: 0.8686 (t80) REVERT: E 123 MET cc_start: 0.9266 (mtm) cc_final: 0.8958 (mtm) outliers start: 45 outliers final: 14 residues processed: 154 average time/residue: 0.1768 time to fit residues: 43.3032 Evaluate side-chains 134 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 1102 MET Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 107 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 284 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 267 optimal weight: 50.0000 chunk 186 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 279 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 705 HIS C 793 ASN D 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.057907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.043321 restraints weight = 134060.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.044439 restraints weight = 76484.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.045108 restraints weight = 52991.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.045551 restraints weight = 42543.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.045796 restraints weight = 37131.956| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24638 Z= 0.185 Angle : 0.572 9.388 33411 Z= 0.285 Chirality : 0.041 0.192 3657 Planarity : 0.004 0.058 4403 Dihedral : 4.143 43.378 3315 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 1.29 % Allowed : 10.30 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.15), residues: 2996 helix: 1.69 (0.13), residues: 1543 sheet: 0.27 (0.30), residues: 271 loop : -0.51 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 668 TYR 0.016 0.001 TYR B1111 PHE 0.013 0.001 PHE C 849 TRP 0.012 0.001 TRP B1085 HIS 0.006 0.001 HIS B1133 Details of bonding type rmsd covalent geometry : bond 0.00405 (24638) covalent geometry : angle 0.57231 (33411) hydrogen bonds : bond 0.03603 ( 1175) hydrogen bonds : angle 4.18848 ( 3396) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.8632 (pttp) cc_final: 0.8320 (pttm) REVERT: B 504 MET cc_start: 0.9088 (tpp) cc_final: 0.8334 (tpp) REVERT: B 658 MET cc_start: 0.8793 (mmm) cc_final: 0.8522 (mmt) REVERT: B 1021 MET cc_start: 0.7683 (tmm) cc_final: 0.5919 (tmm) REVERT: B 1061 MET cc_start: 0.8405 (mmm) cc_final: 0.7457 (mmm) REVERT: B 1102 MET cc_start: 0.7850 (ppp) cc_final: 0.7477 (ppp) REVERT: B 1171 MET cc_start: 0.8571 (ptm) cc_final: 0.8103 (ppp) REVERT: C 34 MET cc_start: 0.8207 (mmm) cc_final: 0.7790 (tpp) REVERT: C 96 MET cc_start: 0.9108 (mmm) cc_final: 0.8682 (tpt) REVERT: C 397 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8783 (mm) REVERT: C 680 MET cc_start: 0.8958 (mmm) cc_final: 0.8618 (mmm) REVERT: C 787 MET cc_start: 0.8232 (mpp) cc_final: 0.7717 (mpp) REVERT: C 1079 MET cc_start: 0.7749 (pmm) cc_final: 0.7347 (pmm) REVERT: C 1102 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8569 (ppp) REVERT: D 273 MET cc_start: 0.8232 (mpp) cc_final: 0.7290 (mpp) REVERT: D 483 MET cc_start: 0.6342 (ppp) cc_final: 0.5927 (ppp) REVERT: D 518 ASN cc_start: 0.7895 (m-40) cc_final: 0.7643 (t0) REVERT: D 536 MET cc_start: 0.7526 (tpp) cc_final: 0.7224 (tpp) REVERT: A 41 MET cc_start: 0.7015 (tpp) cc_final: 0.6791 (tpp) REVERT: A 116 MET cc_start: 0.8821 (mmm) cc_final: 0.8187 (mmm) REVERT: E 70 GLU cc_start: 0.8767 (pp20) cc_final: 0.8374 (tm-30) REVERT: E 116 MET cc_start: 0.8945 (tpp) cc_final: 0.8362 (mmm) REVERT: E 122 TYR cc_start: 0.9045 (t80) cc_final: 0.8659 (t80) REVERT: E 123 MET cc_start: 0.9384 (mtm) cc_final: 0.9037 (mtm) outliers start: 33 outliers final: 16 residues processed: 150 average time/residue: 0.1538 time to fit residues: 37.9205 Evaluate side-chains 133 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 1102 MET Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 107 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 57 optimal weight: 8.9990 chunk 232 optimal weight: 9.9990 chunk 247 optimal weight: 9.9990 chunk 52 optimal weight: 30.0000 chunk 19 optimal weight: 0.2980 chunk 190 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 chunk 155 optimal weight: 0.7980 chunk 92 optimal weight: 8.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 875 ASN C 757 GLN C 792 GLN C 881 ASN A 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.057885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.043405 restraints weight = 135277.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.044538 restraints weight = 75602.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.045220 restraints weight = 52714.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.045649 restraints weight = 42264.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.045855 restraints weight = 36990.430| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24638 Z= 0.168 Angle : 0.579 12.504 33411 Z= 0.285 Chirality : 0.041 0.259 3657 Planarity : 0.004 0.053 4403 Dihedral : 4.102 43.096 3315 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.57 % Favored : 96.36 % Rotamer: Outliers : 1.13 % Allowed : 10.77 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.15), residues: 2996 helix: 1.76 (0.13), residues: 1549 sheet: 0.29 (0.30), residues: 272 loop : -0.54 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 272 TYR 0.015 0.001 TYR B1111 PHE 0.015 0.001 PHE C 62 TRP 0.012 0.001 TRP B1085 HIS 0.005 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00371 (24638) covalent geometry : angle 0.57936 (33411) hydrogen bonds : bond 0.03528 ( 1175) hydrogen bonds : angle 4.15558 ( 3396) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8261 (tm-30) REVERT: B 264 LYS cc_start: 0.8581 (pttp) cc_final: 0.8290 (pttp) REVERT: B 658 MET cc_start: 0.8774 (mmm) cc_final: 0.8511 (mmt) REVERT: B 1021 MET cc_start: 0.7712 (tmm) cc_final: 0.5526 (tmm) REVERT: B 1061 MET cc_start: 0.8381 (mmm) cc_final: 0.7407 (mmm) REVERT: B 1168 MET cc_start: 0.7680 (ttm) cc_final: 0.7214 (ttm) REVERT: B 1171 MET cc_start: 0.8547 (ptm) cc_final: 0.8128 (ppp) REVERT: C 34 MET cc_start: 0.8311 (mmm) cc_final: 0.7895 (tpp) REVERT: C 96 MET cc_start: 0.9101 (mmm) cc_final: 0.8669 (tpt) REVERT: C 397 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8760 (mm) REVERT: C 667 MET cc_start: 0.8505 (mmt) cc_final: 0.8207 (mmt) REVERT: C 680 MET cc_start: 0.9006 (mmm) cc_final: 0.8655 (mmm) REVERT: C 787 MET cc_start: 0.8192 (mpp) cc_final: 0.7679 (mpp) REVERT: C 1079 MET cc_start: 0.7592 (pmm) cc_final: 0.7352 (pmm) REVERT: D 273 MET cc_start: 0.8113 (mpp) cc_final: 0.7229 (mpp) REVERT: D 279 MET cc_start: 0.9223 (tpp) cc_final: 0.8778 (tpp) REVERT: D 462 MET cc_start: 0.3261 (ppp) cc_final: 0.2824 (ppp) REVERT: D 483 MET cc_start: 0.6324 (ppp) cc_final: 0.5899 (ppp) REVERT: D 518 ASN cc_start: 0.7706 (m-40) cc_final: 0.7415 (t0) REVERT: D 536 MET cc_start: 0.7563 (tpp) cc_final: 0.7247 (tpp) REVERT: A 116 MET cc_start: 0.8771 (mmm) cc_final: 0.8440 (mmm) REVERT: E 70 GLU cc_start: 0.8696 (pp20) cc_final: 0.8248 (tm-30) REVERT: E 75 MET cc_start: 0.9216 (mpp) cc_final: 0.8953 (mpp) REVERT: E 111 GLU cc_start: 0.8525 (pm20) cc_final: 0.8298 (pm20) REVERT: E 116 MET cc_start: 0.8937 (tpp) cc_final: 0.8382 (mmm) REVERT: E 122 TYR cc_start: 0.9049 (t80) cc_final: 0.8641 (t80) outliers start: 29 outliers final: 18 residues processed: 143 average time/residue: 0.1535 time to fit residues: 36.6151 Evaluate side-chains 134 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 882 ASP Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 107 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 160 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 80 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 162 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 chunk 274 optimal weight: 30.0000 chunk 3 optimal weight: 9.9990 chunk 230 optimal weight: 30.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.057830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.043354 restraints weight = 135144.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.044486 restraints weight = 75590.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.045194 restraints weight = 52268.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.045562 restraints weight = 42054.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.045830 restraints weight = 37096.684| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24638 Z= 0.160 Angle : 0.570 12.240 33411 Z= 0.281 Chirality : 0.040 0.255 3657 Planarity : 0.004 0.048 4403 Dihedral : 4.062 43.015 3315 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.50 % Favored : 96.43 % Rotamer: Outliers : 1.13 % Allowed : 10.73 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.15), residues: 2996 helix: 1.82 (0.13), residues: 1555 sheet: 0.34 (0.31), residues: 272 loop : -0.52 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 272 TYR 0.014 0.001 TYR B1111 PHE 0.010 0.001 PHE C 240 TRP 0.011 0.001 TRP B1085 HIS 0.005 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00355 (24638) covalent geometry : angle 0.56974 (33411) hydrogen bonds : bond 0.03440 ( 1175) hydrogen bonds : angle 4.11108 ( 3396) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: B 264 LYS cc_start: 0.8631 (pttp) cc_final: 0.8335 (pttp) REVERT: B 658 MET cc_start: 0.8768 (mmm) cc_final: 0.8507 (mmt) REVERT: B 1021 MET cc_start: 0.7395 (tmm) cc_final: 0.5631 (tmm) REVERT: B 1061 MET cc_start: 0.8368 (mmm) cc_final: 0.7465 (mmm) REVERT: B 1168 MET cc_start: 0.7702 (ttm) cc_final: 0.7226 (ttm) REVERT: B 1171 MET cc_start: 0.8677 (ptm) cc_final: 0.8307 (ppp) REVERT: C 34 MET cc_start: 0.8303 (mmm) cc_final: 0.7822 (tpp) REVERT: C 96 MET cc_start: 0.9097 (mmm) cc_final: 0.8666 (tpt) REVERT: C 397 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8740 (mm) REVERT: C 667 MET cc_start: 0.8533 (mmt) cc_final: 0.8179 (mmt) REVERT: C 680 MET cc_start: 0.8931 (mmm) cc_final: 0.8555 (mmm) REVERT: C 787 MET cc_start: 0.8174 (mpp) cc_final: 0.7638 (mpp) REVERT: C 1102 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8537 (ppp) REVERT: D 273 MET cc_start: 0.7985 (mpp) cc_final: 0.7213 (mpp) REVERT: D 279 MET cc_start: 0.9271 (tpp) cc_final: 0.8880 (tpp) REVERT: D 462 MET cc_start: 0.3339 (ppp) cc_final: 0.2961 (ppp) REVERT: D 483 MET cc_start: 0.6277 (ppp) cc_final: 0.5877 (ppp) REVERT: D 536 MET cc_start: 0.7561 (tpp) cc_final: 0.7246 (tpp) REVERT: A 116 MET cc_start: 0.8726 (mmm) cc_final: 0.8259 (mmm) REVERT: E 70 GLU cc_start: 0.8724 (pp20) cc_final: 0.8303 (tm-30) REVERT: E 111 GLU cc_start: 0.8507 (pm20) cc_final: 0.8271 (pm20) REVERT: E 116 MET cc_start: 0.8885 (tpp) cc_final: 0.8283 (mmm) REVERT: E 122 TYR cc_start: 0.9027 (t80) cc_final: 0.8615 (t80) REVERT: E 123 MET cc_start: 0.9315 (mtm) cc_final: 0.9063 (mtm) outliers start: 29 outliers final: 17 residues processed: 140 average time/residue: 0.1490 time to fit residues: 34.6009 Evaluate side-chains 131 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 882 ASP Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 1102 MET Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 107 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 142 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 275 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 226 optimal weight: 0.8980 chunk 160 optimal weight: 9.9990 chunk 215 optimal weight: 0.0770 chunk 217 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 overall best weight: 2.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 757 GLN C 793 ASN C 817 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.058510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.044049 restraints weight = 135323.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.045207 restraints weight = 75240.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.045864 restraints weight = 51733.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.046331 restraints weight = 41825.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.046567 restraints weight = 36234.387| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24638 Z= 0.109 Angle : 0.547 13.443 33411 Z= 0.265 Chirality : 0.040 0.264 3657 Planarity : 0.003 0.047 4403 Dihedral : 3.911 41.957 3315 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.17 % Favored : 96.76 % Rotamer: Outliers : 0.94 % Allowed : 10.92 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.16), residues: 2996 helix: 2.00 (0.13), residues: 1546 sheet: 0.42 (0.32), residues: 261 loop : -0.47 (0.18), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 272 TYR 0.019 0.001 TYR D 108 PHE 0.009 0.001 PHE B 257 TRP 0.015 0.001 TRP B1085 HIS 0.004 0.001 HIS E 91 Details of bonding type rmsd covalent geometry : bond 0.00239 (24638) covalent geometry : angle 0.54682 (33411) hydrogen bonds : bond 0.03164 ( 1175) hydrogen bonds : angle 4.00450 ( 3396) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.8608 (pttp) cc_final: 0.8274 (pttp) REVERT: B 431 MET cc_start: 0.8130 (mtp) cc_final: 0.7817 (mtm) REVERT: B 1021 MET cc_start: 0.7167 (tmm) cc_final: 0.5444 (tmm) REVERT: B 1061 MET cc_start: 0.8317 (mmm) cc_final: 0.7502 (mmm) REVERT: B 1171 MET cc_start: 0.8651 (ptm) cc_final: 0.8247 (ppp) REVERT: C 34 MET cc_start: 0.8276 (mmm) cc_final: 0.7899 (tpp) REVERT: C 96 MET cc_start: 0.9061 (mmm) cc_final: 0.8642 (tpt) REVERT: C 397 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8634 (mm) REVERT: C 667 MET cc_start: 0.8502 (mmt) cc_final: 0.8132 (mmp) REVERT: C 680 MET cc_start: 0.8913 (mmm) cc_final: 0.8545 (mmm) REVERT: C 787 MET cc_start: 0.8142 (mpp) cc_final: 0.7602 (mpp) REVERT: D 273 MET cc_start: 0.7986 (mpp) cc_final: 0.7189 (mpp) REVERT: D 279 MET cc_start: 0.9229 (tpp) cc_final: 0.8785 (tpp) REVERT: D 462 MET cc_start: 0.3243 (ppp) cc_final: 0.2883 (ppp) REVERT: D 483 MET cc_start: 0.6100 (ppp) cc_final: 0.5806 (ppp) REVERT: A 99 LYS cc_start: 0.9388 (mmtm) cc_final: 0.9044 (mmtm) REVERT: A 116 MET cc_start: 0.8691 (mmm) cc_final: 0.8184 (mmm) REVERT: E 70 GLU cc_start: 0.8696 (pp20) cc_final: 0.8257 (tm-30) REVERT: E 75 MET cc_start: 0.9200 (mpp) cc_final: 0.8778 (mpp) REVERT: E 116 MET cc_start: 0.8913 (tpp) cc_final: 0.8400 (mmm) REVERT: E 122 TYR cc_start: 0.9010 (t80) cc_final: 0.8593 (t80) outliers start: 24 outliers final: 16 residues processed: 140 average time/residue: 0.1725 time to fit residues: 39.7078 Evaluate side-chains 132 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 107 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 157 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 167 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 485 GLN B 496 GLN ** B1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN C 793 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.057080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.042702 restraints weight = 136649.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.043832 restraints weight = 76672.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.044529 restraints weight = 53387.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.044885 restraints weight = 42447.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.045187 restraints weight = 37509.074| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24638 Z= 0.219 Angle : 0.646 21.593 33411 Z= 0.318 Chirality : 0.042 0.276 3657 Planarity : 0.004 0.048 4403 Dihedral : 4.211 43.592 3315 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.97 % Favored : 95.99 % Rotamer: Outliers : 0.78 % Allowed : 11.08 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.15), residues: 2996 helix: 1.74 (0.13), residues: 1547 sheet: 0.35 (0.31), residues: 274 loop : -0.57 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 272 TYR 0.018 0.001 TYR D 108 PHE 0.012 0.002 PHE C 421 TRP 0.056 0.002 TRP B 168 HIS 0.006 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00482 (24638) covalent geometry : angle 0.64584 (33411) hydrogen bonds : bond 0.03745 ( 1175) hydrogen bonds : angle 4.32150 ( 3396) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 504 MET cc_start: 0.9392 (tpp) cc_final: 0.8797 (tpp) REVERT: B 518 MET cc_start: 0.9232 (mmm) cc_final: 0.8818 (mmm) REVERT: B 660 MET cc_start: 0.8621 (ttp) cc_final: 0.8089 (ttp) REVERT: B 1021 MET cc_start: 0.7186 (tmm) cc_final: 0.5553 (tmm) REVERT: B 1061 MET cc_start: 0.8425 (mmm) cc_final: 0.7578 (mmm) REVERT: B 1171 MET cc_start: 0.8644 (ptm) cc_final: 0.8273 (ppp) REVERT: C 34 MET cc_start: 0.8366 (mmm) cc_final: 0.7954 (tpp) REVERT: C 96 MET cc_start: 0.9099 (mmm) cc_final: 0.8743 (tpt) REVERT: C 397 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8686 (mm) REVERT: C 667 MET cc_start: 0.8524 (mmt) cc_final: 0.8153 (mmt) REVERT: C 680 MET cc_start: 0.8955 (mmm) cc_final: 0.8594 (mmm) REVERT: C 787 MET cc_start: 0.8140 (mpp) cc_final: 0.7641 (mpp) REVERT: D 273 MET cc_start: 0.7978 (mpp) cc_final: 0.7169 (mpp) REVERT: D 279 MET cc_start: 0.9268 (tpp) cc_final: 0.9003 (tpp) REVERT: D 462 MET cc_start: 0.3322 (ppp) cc_final: 0.2947 (ppp) REVERT: D 483 MET cc_start: 0.5978 (ppp) cc_final: 0.5688 (ppp) REVERT: D 536 MET cc_start: 0.7249 (tpp) cc_final: 0.6763 (tpp) REVERT: A 99 LYS cc_start: 0.9433 (mmtm) cc_final: 0.9111 (mmtm) REVERT: A 116 MET cc_start: 0.8696 (mmm) cc_final: 0.8270 (mmm) REVERT: E 70 GLU cc_start: 0.8763 (pp20) cc_final: 0.8371 (tm-30) REVERT: E 75 MET cc_start: 0.9280 (mpp) cc_final: 0.8880 (mpp) REVERT: E 116 MET cc_start: 0.8961 (tpp) cc_final: 0.8316 (tpp) REVERT: E 122 TYR cc_start: 0.9040 (t80) cc_final: 0.8606 (t80) outliers start: 20 outliers final: 16 residues processed: 134 average time/residue: 0.1653 time to fit residues: 36.9379 Evaluate side-chains 132 residues out of total 2563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 1109 LEU Chi-restraints excluded: chain B residue 1118 LEU Chi-restraints excluded: chain B residue 1158 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 941 MET Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain E residue 107 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 149 optimal weight: 0.4980 chunk 115 optimal weight: 7.9990 chunk 239 optimal weight: 10.0000 chunk 199 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 284 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 485 GLN B1018 GLN C 793 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.058888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.044484 restraints weight = 132187.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.045676 restraints weight = 71549.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.046383 restraints weight = 48647.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.046829 restraints weight = 38694.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.047067 restraints weight = 33383.054| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24638 Z= 0.098 Angle : 0.564 19.136 33411 Z= 0.273 Chirality : 0.040 0.254 3657 Planarity : 0.003 0.049 4403 Dihedral : 3.911 41.114 3315 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.90 % Favored : 97.03 % Rotamer: Outliers : 0.62 % Allowed : 11.39 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.16), residues: 2996 helix: 2.05 (0.13), residues: 1545 sheet: 0.46 (0.32), residues: 259 loop : -0.45 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 272 TYR 0.014 0.001 TYR B1111 PHE 0.014 0.001 PHE B 257 TRP 0.041 0.001 TRP B 168 HIS 0.004 0.001 HIS C 563 Details of bonding type rmsd covalent geometry : bond 0.00212 (24638) covalent geometry : angle 0.56370 (33411) hydrogen bonds : bond 0.03089 ( 1175) hydrogen bonds : angle 4.01159 ( 3396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3392.35 seconds wall clock time: 59 minutes 41.94 seconds (3581.94 seconds total)