Starting phenix.real_space_refine on Thu Feb 5 12:20:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hms_52297/02_2026/9hms_52297.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hms_52297/02_2026/9hms_52297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hms_52297/02_2026/9hms_52297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hms_52297/02_2026/9hms_52297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hms_52297/02_2026/9hms_52297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hms_52297/02_2026/9hms_52297.map" } resolution = 3.4 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= -0.022 sd= 0.291 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 86 5.16 5 C 10751 2.51 5 N 2911 2.21 5 O 3160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16909 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 933, 7178 Classifications: {'peptide': 933} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 18, 'TRANS': 914} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 430 Unresolved non-hydrogen angles: 544 Unresolved non-hydrogen dihedrals: 367 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'PHE:plan': 8, 'GLU:plan': 9, 'GLN:plan1': 6, 'ASP:plan': 10, 'TRP:plan': 2, 'TYR:plan': 5, 'HIS:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 242 Chain: "B" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 869 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 8861 Classifications: {'peptide': 1141} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1083} Chain breaks: 7 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11736 SG CYS C1146 75.574 87.193 165.337 1.00 30.00 S ATOM 11750 SG CYS C1148 75.473 90.964 164.620 1.00 30.00 S ATOM 11770 SG CYS C1151 72.657 88.550 163.383 1.00 30.00 S Time building chain proxies: 3.59, per 1000 atoms: 0.21 Number of scatterers: 16909 At special positions: 0 Unit cell: (87.5328, 139.872, 219.283, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 86 16.00 O 3160 8.00 N 2911 7.00 C 10751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 637 " - pdb=" SG CYS C 687 " distance=2.04 Simple disulfide: pdb=" SG CYS C1578 " - pdb=" SG CYS C1607 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 709.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C2201 " pdb="ZN ZN C2201 " - pdb=" ND1 HIS C1142 " pdb="ZN ZN C2201 " - pdb=" SG CYS C1146 " pdb="ZN ZN C2201 " - pdb=" SG CYS C1151 " pdb="ZN ZN C2201 " - pdb=" SG CYS C1148 " Number of angles added : 3 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4176 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 2 sheets defined 70.8% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 95 through 109 removed outlier: 3.556A pdb=" N HIS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 124 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.833A pdb=" N LYS A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 187 removed outlier: 3.984A pdb=" N PHE A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 210 removed outlier: 3.579A pdb=" N SER A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 250 removed outlier: 4.197A pdb=" N THR A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 292 removed outlier: 3.743A pdb=" N GLN A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 301 through 319 removed outlier: 3.864A pdb=" N ARG A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 341 through 356 removed outlier: 3.723A pdb=" N LEU A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.823A pdb=" N GLU A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASP A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.599A pdb=" N ALA A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 388 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLN A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 396 " --> pdb=" O LYS A 392 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 416 removed outlier: 3.691A pdb=" N VAL A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.662A pdb=" N ALA A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 removed outlier: 3.709A pdb=" N LEU A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 465 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 Processing helix chain 'A' and resid 494 through 504 removed outlier: 3.841A pdb=" N MET A 498 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 502 " --> pdb=" O MET A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 534 Processing helix chain 'A' and resid 549 through 578 removed outlier: 4.914A pdb=" N VAL A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Proline residue: A 572 - end of helix Processing helix chain 'A' and resid 581 through 589 Processing helix chain 'A' and resid 590 through 595 Processing helix chain 'A' and resid 597 through 602 removed outlier: 4.094A pdb=" N THR A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 621 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 646 through 674 removed outlier: 3.685A pdb=" N ASP A 671 " --> pdb=" O ARG A 667 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 674 " --> pdb=" O GLU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 698 Processing helix chain 'A' and resid 708 through 723 Processing helix chain 'A' and resid 726 through 747 removed outlier: 3.653A pdb=" N HIS A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 777 removed outlier: 3.709A pdb=" N LEU A 758 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 777 " --> pdb=" O GLN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 798 Processing helix chain 'A' and resid 799 through 804 removed outlier: 3.690A pdb=" N MET A 803 " --> pdb=" O HIS A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 811 removed outlier: 3.832A pdb=" N LEU A 810 " --> pdb=" O ARG A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 833 removed outlier: 3.629A pdb=" N LEU A 826 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 874 Processing helix chain 'A' and resid 878 through 881 Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 888 through 893 removed outlier: 4.108A pdb=" N LYS A 891 " --> pdb=" O GLN A 888 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A 892 " --> pdb=" O TYR A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 911 removed outlier: 3.892A pdb=" N GLN A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 911 " --> pdb=" O THR A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 932 Processing helix chain 'A' and resid 943 through 959 removed outlier: 3.508A pdb=" N ARG A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 959 " --> pdb=" O PHE A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 982 Processing helix chain 'A' and resid 998 through 1004 removed outlier: 3.984A pdb=" N ILE A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1010 removed outlier: 4.463A pdb=" N SER A1008 " --> pdb=" O GLU A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1027 removed outlier: 3.579A pdb=" N LYS A1024 " --> pdb=" O VAL A1020 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE A1025 " --> pdb=" O TYR A1021 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR A1027 " --> pdb=" O GLU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1035 through 1037 No H-bonds generated for 'chain 'A' and resid 1035 through 1037' Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 357 through 367 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 413 through 420 removed outlier: 4.051A pdb=" N GLU B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 595 Processing helix chain 'C' and resid 599 through 614 Processing helix chain 'C' and resid 618 through 637 Processing helix chain 'C' and resid 641 through 646 Processing helix chain 'C' and resid 648 through 661 Processing helix chain 'C' and resid 669 through 703 Processing helix chain 'C' and resid 730 through 735 removed outlier: 3.742A pdb=" N ALA C 734 " --> pdb=" O TYR C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 758 removed outlier: 3.680A pdb=" N SER C 744 " --> pdb=" O ASP C 740 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS C 745 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 747 " --> pdb=" O GLN C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 786 removed outlier: 3.949A pdb=" N THR C 772 " --> pdb=" O CYS C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 806 removed outlier: 3.615A pdb=" N GLU C 794 " --> pdb=" O MET C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 827 removed outlier: 3.681A pdb=" N ALA C 812 " --> pdb=" O ASP C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 843 removed outlier: 3.699A pdb=" N ALA C 832 " --> pdb=" O CYS C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 871 Processing helix chain 'C' and resid 873 through 887 removed outlier: 3.722A pdb=" N SER C 879 " --> pdb=" O THR C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 892 Processing helix chain 'C' and resid 894 through 913 removed outlier: 3.775A pdb=" N VAL C 902 " --> pdb=" O TYR C 898 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN C 903 " --> pdb=" O LEU C 899 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA C 909 " --> pdb=" O LEU C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 931 removed outlier: 4.117A pdb=" N GLN C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 934 through 954 removed outlier: 3.821A pdb=" N ALA C 938 " --> pdb=" O THR C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 1002 removed outlier: 3.658A pdb=" N VAL C 978 " --> pdb=" O GLY C 974 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TRP C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1022 Processing helix chain 'C' and resid 1023 through 1041 removed outlier: 3.808A pdb=" N LYS C1034 " --> pdb=" O PHE C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1043 through 1062 Processing helix chain 'C' and resid 1148 through 1153 removed outlier: 3.513A pdb=" N SER C1153 " --> pdb=" O SER C1149 " (cutoff:3.500A) Processing helix chain 'C' and resid 1153 through 1175 removed outlier: 3.527A pdb=" N GLY C1175 " --> pdb=" O ARG C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1207 Proline residue: C1192 - end of helix Processing helix chain 'C' and resid 1219 through 1237 removed outlier: 3.694A pdb=" N ASN C1236 " --> pdb=" O LEU C1232 " (cutoff:3.500A) Processing helix chain 'C' and resid 1241 through 1256 removed outlier: 3.729A pdb=" N LEU C1247 " --> pdb=" O LEU C1243 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN C1248 " --> pdb=" O GLN C1244 " (cutoff:3.500A) Processing helix chain 'C' and resid 1261 through 1278 removed outlier: 3.631A pdb=" N ARG C1265 " --> pdb=" O LEU C1261 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY C1278 " --> pdb=" O LEU C1274 " (cutoff:3.500A) Processing helix chain 'C' and resid 1573 through 1590 removed outlier: 4.837A pdb=" N HIS C1590 " --> pdb=" O ARG C1586 " (cutoff:3.500A) Processing helix chain 'C' and resid 1593 through 1609 Processing helix chain 'C' and resid 1612 through 1622 Processing helix chain 'C' and resid 1625 through 1642 removed outlier: 3.701A pdb=" N ARG C1629 " --> pdb=" O SER C1625 " (cutoff:3.500A) Processing helix chain 'C' and resid 1668 through 1678 Processing helix chain 'C' and resid 1691 through 1700 Processing helix chain 'C' and resid 1749 through 1768 removed outlier: 3.513A pdb=" N VAL C1753 " --> pdb=" O HIS C1749 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU C1754 " --> pdb=" O LEU C1750 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP C1758 " --> pdb=" O LEU C1754 " (cutoff:3.500A) Processing helix chain 'C' and resid 1772 through 1797 removed outlier: 3.962A pdb=" N HIS C1785 " --> pdb=" O LEU C1781 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG C1786 " --> pdb=" O ALA C1782 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C1792 " --> pdb=" O GLU C1788 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU C1795 " --> pdb=" O ILE C1791 " (cutoff:3.500A) Processing helix chain 'C' and resid 1814 through 1818 removed outlier: 3.530A pdb=" N GLN C1817 " --> pdb=" O GLY C1814 " (cutoff:3.500A) Processing helix chain 'C' and resid 1825 through 1830 Processing helix chain 'C' and resid 1845 through 1849 Processing helix chain 'C' and resid 1850 through 1862 Processing helix chain 'C' and resid 1865 through 1880 removed outlier: 4.021A pdb=" N GLN C1870 " --> pdb=" O PRO C1866 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU C1873 " --> pdb=" O ALA C1869 " (cutoff:3.500A) Processing helix chain 'C' and resid 1920 through 1933 removed outlier: 3.797A pdb=" N LEU C1924 " --> pdb=" O SER C1920 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C1928 " --> pdb=" O LEU C1924 " (cutoff:3.500A) Processing helix chain 'C' and resid 1936 through 1941 removed outlier: 3.629A pdb=" N SER C1940 " --> pdb=" O SER C1936 " (cutoff:3.500A) Processing helix chain 'C' and resid 1958 through 1965 removed outlier: 3.671A pdb=" N GLU C1962 " --> pdb=" O LEU C1958 " (cutoff:3.500A) Processing helix chain 'C' and resid 1966 through 1972 removed outlier: 3.634A pdb=" N GLU C1972 " --> pdb=" O ASN C1968 " (cutoff:3.500A) Processing helix chain 'C' and resid 1984 through 1995 Processing helix chain 'C' and resid 2011 through 2017 Processing helix chain 'C' and resid 2045 through 2050 Processing helix chain 'C' and resid 2051 through 2053 No H-bonds generated for 'chain 'C' and resid 2051 through 2053' Processing helix chain 'C' and resid 2065 through 2084 removed outlier: 4.005A pdb=" N ILE C2069 " --> pdb=" O THR C2065 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY C2084 " --> pdb=" O TRP C2080 " (cutoff:3.500A) Processing helix chain 'C' and resid 2088 through 2097 removed outlier: 3.821A pdb=" N TYR C2092 " --> pdb=" O PRO C2088 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 1734 through 1740 removed outlier: 6.080A pdb=" N GLU C1731 " --> pdb=" O PRO C1735 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL C1737 " --> pdb=" O ARG C1729 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C1724 " --> pdb=" O ALA C1714 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C1728 " --> pdb=" O VAL C1710 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C1710 " --> pdb=" O THR C1728 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 1975 through 1979 removed outlier: 3.586A pdb=" N ARG C1976 " --> pdb=" O THR C1948 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N TYR C1998 " --> pdb=" O LEU C2025 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N PHE C2027 " --> pdb=" O TYR C1998 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR C2000 " --> pdb=" O PHE C2027 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA C2024 " --> pdb=" O LEU C2058 " (cutoff:3.500A) 1025 hydrogen bonds defined for protein. 3015 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: 2.89 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3121 1.32 - 1.45: 4055 1.45 - 1.57: 9912 1.57 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 17210 Sorted by residual: bond pdb=" C THR A 789 " pdb=" O THR A 789 " ideal model delta sigma weight residual 1.236 1.283 -0.047 1.15e-02 7.56e+03 1.64e+01 bond pdb=" N VAL C1798 " pdb=" CA VAL C1798 " ideal model delta sigma weight residual 1.459 1.506 -0.046 1.21e-02 6.83e+03 1.45e+01 bond pdb=" N GLY A 806 " pdb=" CA GLY A 806 " ideal model delta sigma weight residual 1.444 1.483 -0.039 1.02e-02 9.61e+03 1.44e+01 bond pdb=" C ALA A 477 " pdb=" O ALA A 477 " ideal model delta sigma weight residual 1.236 1.285 -0.050 1.39e-02 5.18e+03 1.28e+01 bond pdb=" N ILE B 347 " pdb=" CA ILE B 347 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.25e+01 ... (remaining 17205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 21773 2.06 - 4.12: 1389 4.12 - 6.18: 154 6.18 - 8.24: 17 8.24 - 10.30: 10 Bond angle restraints: 23343 Sorted by residual: angle pdb=" N TYR C 730 " pdb=" CA TYR C 730 " pdb=" C TYR C 730 " ideal model delta sigma weight residual 113.50 105.31 8.19 1.23e+00 6.61e-01 4.44e+01 angle pdb=" N PRO B 395 " pdb=" CA PRO B 395 " pdb=" CB PRO B 395 " ideal model delta sigma weight residual 103.00 110.26 -7.26 1.10e+00 8.26e-01 4.36e+01 angle pdb=" N PHE C2027 " pdb=" CA PHE C2027 " pdb=" CB PHE C2027 " ideal model delta sigma weight residual 110.49 101.77 8.72 1.47e+00 4.63e-01 3.52e+01 angle pdb=" C TYR A 479 " pdb=" CA TYR A 479 " pdb=" CB TYR A 479 " ideal model delta sigma weight residual 110.85 119.95 -9.10 1.70e+00 3.46e-01 2.86e+01 angle pdb=" N VAL C1798 " pdb=" CA VAL C1798 " pdb=" C VAL C1798 " ideal model delta sigma weight residual 110.82 116.01 -5.19 9.70e-01 1.06e+00 2.86e+01 ... (remaining 23338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 9332 17.89 - 35.77: 820 35.77 - 53.66: 206 53.66 - 71.54: 119 71.54 - 89.43: 8 Dihedral angle restraints: 10485 sinusoidal: 4085 harmonic: 6400 Sorted by residual: dihedral pdb=" CB CYS C 637 " pdb=" SG CYS C 637 " pdb=" SG CYS C 687 " pdb=" CB CYS C 687 " ideal model delta sinusoidal sigma weight residual -86.00 -153.32 67.32 1 1.00e+01 1.00e-02 5.90e+01 dihedral pdb=" CB CYS C1578 " pdb=" SG CYS C1578 " pdb=" SG CYS C1607 " pdb=" CB CYS C1607 " ideal model delta sinusoidal sigma weight residual 93.00 150.25 -57.25 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CA GLU A 194 " pdb=" C GLU A 194 " pdb=" N TYR A 195 " pdb=" CA TYR A 195 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 10482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2126 0.060 - 0.121: 485 0.121 - 0.181: 96 0.181 - 0.241: 20 0.241 - 0.302: 2 Chirality restraints: 2729 Sorted by residual: chirality pdb=" CA VAL B 425 " pdb=" N VAL B 425 " pdb=" C VAL B 425 " pdb=" CB VAL B 425 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA PRO B 395 " pdb=" N PRO B 395 " pdb=" C PRO B 395 " pdb=" CB PRO B 395 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA MET A 224 " pdb=" N MET A 224 " pdb=" C MET A 224 " pdb=" CB MET A 224 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 2726 not shown) Planarity restraints: 2982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 984 " -0.076 5.00e-02 4.00e+02 1.12e-01 2.02e+01 pdb=" N PRO A 985 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO A 985 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 985 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 798 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.86e+01 pdb=" C PHE A 798 " -0.075 2.00e-02 2.50e+03 pdb=" O PHE A 798 " 0.027 2.00e-02 2.50e+03 pdb=" N SER A 799 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C2004 " 0.016 2.00e-02 2.50e+03 3.07e-02 9.45e+00 pdb=" C GLY C2004 " -0.053 2.00e-02 2.50e+03 pdb=" O GLY C2004 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA C2005 " 0.017 2.00e-02 2.50e+03 ... (remaining 2979 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3400 2.78 - 3.31: 17279 3.31 - 3.84: 27559 3.84 - 4.37: 32985 4.37 - 4.90: 53714 Nonbonded interactions: 134937 Sorted by model distance: nonbonded pdb=" OH TYR A 297 " pdb=" O TYR A 331 " model vdw 2.251 3.040 nonbonded pdb=" O GLY C1609 " pdb=" OG1 THR C1616 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP A 659 " pdb=" NE1 TRP A 706 " model vdw 2.277 3.120 nonbonded pdb=" O ASP A 299 " pdb=" NH1 ARG A 305 " model vdw 2.282 3.120 nonbonded pdb=" O PHE C1288 " pdb=" OG SER C1291 " model vdw 2.299 3.040 ... (remaining 134932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.81 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.400 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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 : 0.007 0.072 17216 Z= 0.490 Angle : 1.021 10.302 23350 Z= 0.701 Chirality : 0.055 0.302 2729 Planarity : 0.007 0.112 2982 Dihedral : 16.119 89.430 6303 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.23 % Allowed : 16.28 % Favored : 82.50 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 2152 helix: 0.28 (0.14), residues: 1396 sheet: -1.97 (0.63), residues: 66 loop : -1.98 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1045 TYR 0.016 0.002 TYR A1044 PHE 0.024 0.002 PHE A 647 TRP 0.032 0.002 TRP C 754 HIS 0.016 0.002 HIS C1890 Details of bonding type rmsd covalent geometry : bond 0.00697 (17210) covalent geometry : angle 1.02032 (23343) SS BOND : bond 0.00437 ( 2) SS BOND : angle 0.70878 ( 4) hydrogen bonds : bond 0.16342 ( 1025) hydrogen bonds : angle 5.92579 ( 3015) metal coordination : bond 0.00455 ( 4) metal coordination : angle 2.52369 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 503 time to evaluate : 0.672 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: A 384 TYR cc_start: 0.8387 (m-80) cc_final: 0.8075 (m-10) REVERT: A 604 ARG cc_start: 0.8183 (tpp80) cc_final: 0.7860 (mpt180) REVERT: A 699 ASN cc_start: 0.8116 (t0) cc_final: 0.7803 (t0) REVERT: A 796 MET cc_start: 0.8033 (tpp) cc_final: 0.7750 (tpp) REVERT: A 890 MET cc_start: 0.7284 (mmm) cc_final: 0.6941 (mmm) REVERT: B 352 ASP cc_start: 0.8386 (t0) cc_final: 0.8123 (t0) REVERT: C 693 MET cc_start: 0.6937 (mtp) cc_final: 0.6735 (mtp) REVERT: C 848 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8107 (mm-40) REVERT: C 853 TYR cc_start: 0.7558 (t80) cc_final: 0.7313 (t80) REVERT: C 881 LEU cc_start: 0.8010 (tp) cc_final: 0.7757 (tp) REVERT: C 898 TYR cc_start: 0.6864 (m-10) cc_final: 0.6638 (m-10) REVERT: C 934 THR cc_start: 0.8246 (m) cc_final: 0.7982 (p) REVERT: C 1749 HIS cc_start: 0.5953 (p90) cc_final: 0.5541 (p90) REVERT: C 1872 LEU cc_start: 0.7778 (tp) cc_final: 0.7565 (tp) REVERT: C 1975 TRP cc_start: 0.7194 (m-10) cc_final: 0.6918 (m-10) REVERT: C 2056 LEU cc_start: 0.7917 (tp) cc_final: 0.7155 (tp) outliers start: 22 outliers final: 6 residues processed: 517 average time/residue: 0.1565 time to fit residues: 115.7180 Evaluate side-chains 364 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 358 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 2016 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 0.0050 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 HIS A 352 GLN A 399 GLN A 517 GLN A 608 HIS A 735 GLN ** A 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 601 GLN C 732 ASN C 771 GLN C 791 GLN C 871 HIS C 930 GLN C1022 GLN C1053 GLN ** C1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1635 HIS C1686 HIS C1767 ASN C1957 ASN C1995 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.075829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.066752 restraints weight = 49665.853| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.00 r_work: 0.3031 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17216 Z= 0.163 Angle : 0.651 9.878 23350 Z= 0.333 Chirality : 0.040 0.233 2729 Planarity : 0.005 0.072 2982 Dihedral : 4.638 51.528 2337 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.68 % Allowed : 17.89 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.18), residues: 2152 helix: 1.00 (0.14), residues: 1437 sheet: -1.35 (0.75), residues: 48 loop : -1.81 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 767 TYR 0.022 0.002 TYR A 479 PHE 0.022 0.002 PHE C1618 TRP 0.019 0.002 TRP C 754 HIS 0.017 0.002 HIS C1890 Details of bonding type rmsd covalent geometry : bond 0.00371 (17210) covalent geometry : angle 0.64920 (23343) SS BOND : bond 0.01074 ( 2) SS BOND : angle 2.76927 ( 4) hydrogen bonds : bond 0.05144 ( 1025) hydrogen bonds : angle 4.44777 ( 3015) metal coordination : bond 0.00674 ( 4) metal coordination : angle 2.91754 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 380 time to evaluate : 0.648 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: A 224 MET cc_start: 0.7921 (tpt) cc_final: 0.7685 (tpt) REVERT: A 271 ARG cc_start: 0.8073 (mmt180) cc_final: 0.7851 (mmt180) REVERT: A 272 LYS cc_start: 0.8961 (mttt) cc_final: 0.8731 (mtmm) REVERT: A 285 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7714 (ttp) REVERT: A 472 GLU cc_start: 0.8487 (tt0) cc_final: 0.8113 (tm-30) REVERT: A 473 LEU cc_start: 0.8782 (tp) cc_final: 0.8514 (tt) REVERT: A 583 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8169 (tp30) REVERT: A 604 ARG cc_start: 0.8214 (tpp80) cc_final: 0.7993 (mpt180) REVERT: A 699 ASN cc_start: 0.8560 (t0) cc_final: 0.8307 (t0) REVERT: A 1042 MET cc_start: 0.8666 (tpt) cc_final: 0.8168 (tpt) REVERT: B 412 ASN cc_start: 0.8753 (m-40) cc_final: 0.8339 (m-40) REVERT: C 697 ILE cc_start: 0.8764 (mm) cc_final: 0.8553 (mm) REVERT: C 728 PHE cc_start: 0.6210 (m-80) cc_final: 0.5573 (m-80) REVERT: C 760 LYS cc_start: 0.8809 (pttt) cc_final: 0.8591 (mtmm) REVERT: C 907 LEU cc_start: 0.8445 (tp) cc_final: 0.8065 (tp) REVERT: C 1013 GLU cc_start: 0.8358 (tp30) cc_final: 0.8089 (pp20) REVERT: C 1749 HIS cc_start: 0.7107 (p90) cc_final: 0.6801 (p90) REVERT: C 1818 GLU cc_start: 0.8091 (pt0) cc_final: 0.7732 (pt0) REVERT: C 1826 LEU cc_start: 0.6630 (mt) cc_final: 0.6085 (mt) REVERT: C 1875 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7877 (mm-30) REVERT: C 1880 LEU cc_start: 0.8117 (mp) cc_final: 0.7813 (mp) REVERT: C 1963 GLU cc_start: 0.8365 (tp30) cc_final: 0.8047 (tp30) REVERT: C 2106 ILE cc_start: 0.8853 (mp) cc_final: 0.8602 (mm) outliers start: 84 outliers final: 40 residues processed: 437 average time/residue: 0.1378 time to fit residues: 89.1731 Evaluate side-chains 378 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 337 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 TYR Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 576 TRP Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 1027 CYS Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain C residue 1228 THR Chi-restraints excluded: chain C residue 1583 VAL Chi-restraints excluded: chain C residue 1607 CYS Chi-restraints excluded: chain C residue 1706 VAL Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1741 ILE Chi-restraints excluded: chain C residue 1850 THR Chi-restraints excluded: chain C residue 1970 SER Chi-restraints excluded: chain C residue 2016 LEU Chi-restraints excluded: chain C residue 2039 ASN Chi-restraints excluded: chain C residue 2046 VAL Chi-restraints excluded: chain C residue 2054 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 104 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 175 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 157 optimal weight: 0.0570 chunk 8 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 165 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 623 HIS A 712 ASN A 738 HIS ** A 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 GLN A1029 GLN ** C 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 GLN C 736 ASN C1053 GLN ** C1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1637 HIS C1686 HIS C1870 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.073675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.064595 restraints weight = 50695.205| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.01 r_work: 0.2985 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17216 Z= 0.160 Angle : 0.634 10.754 23350 Z= 0.321 Chirality : 0.039 0.263 2729 Planarity : 0.005 0.065 2982 Dihedral : 4.532 51.597 2333 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.01 % Allowed : 18.51 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 2152 helix: 1.23 (0.14), residues: 1435 sheet: -0.98 (0.76), residues: 48 loop : -1.63 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 338 TYR 0.025 0.002 TYR C2092 PHE 0.024 0.002 PHE C1618 TRP 0.026 0.002 TRP A 315 HIS 0.007 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00367 (17210) covalent geometry : angle 0.63154 (23343) SS BOND : bond 0.00781 ( 2) SS BOND : angle 3.52042 ( 4) hydrogen bonds : bond 0.04903 ( 1025) hydrogen bonds : angle 4.26162 ( 3015) metal coordination : bond 0.00674 ( 4) metal coordination : angle 2.61563 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 360 time to evaluate : 0.822 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: A 272 LYS cc_start: 0.9026 (mttt) cc_final: 0.8775 (mtmm) REVERT: A 276 GLU cc_start: 0.8779 (pp20) cc_final: 0.8530 (pp20) REVERT: A 472 GLU cc_start: 0.8461 (tt0) cc_final: 0.8131 (tm-30) REVERT: A 552 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7389 (mm-30) REVERT: A 649 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8192 (ttp-170) REVERT: A 651 ASP cc_start: 0.8321 (t70) cc_final: 0.8086 (t0) REVERT: A 699 ASN cc_start: 0.8585 (t0) cc_final: 0.8270 (t0) REVERT: A 961 LEU cc_start: 0.7425 (tp) cc_final: 0.6967 (tp) REVERT: A 963 GLN cc_start: 0.7119 (mm-40) cc_final: 0.6431 (mm-40) REVERT: A 1042 MET cc_start: 0.8708 (tpt) cc_final: 0.8243 (tpt) REVERT: B 349 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8284 (p) REVERT: C 760 LYS cc_start: 0.8780 (pttt) cc_final: 0.8571 (mtmm) REVERT: C 1603 PHE cc_start: 0.6743 (t80) cc_final: 0.6499 (t80) REVERT: C 1818 GLU cc_start: 0.8162 (pt0) cc_final: 0.7835 (pt0) REVERT: C 1875 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7931 (mm-30) REVERT: C 1880 LEU cc_start: 0.8284 (mp) cc_final: 0.8079 (mp) REVERT: C 2080 TRP cc_start: 0.8517 (t60) cc_final: 0.8263 (t60) REVERT: C 2106 ILE cc_start: 0.8946 (mp) cc_final: 0.8703 (mm) outliers start: 72 outliers final: 45 residues processed: 404 average time/residue: 0.1414 time to fit residues: 84.2167 Evaluate side-chains 378 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 331 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 649 ARG Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 TYR Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1013 GLN Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 576 TRP Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 1027 CYS Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1055 LEU Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain C residue 1228 THR Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1583 VAL Chi-restraints excluded: chain C residue 1607 CYS Chi-restraints excluded: chain C residue 1706 VAL Chi-restraints excluded: chain C residue 1738 SER Chi-restraints excluded: chain C residue 1741 ILE Chi-restraints excluded: chain C residue 1850 THR Chi-restraints excluded: chain C residue 1873 LEU Chi-restraints excluded: chain C residue 1970 SER Chi-restraints excluded: chain C residue 2016 LEU Chi-restraints excluded: chain C residue 2039 ASN Chi-restraints excluded: chain C residue 2046 VAL Chi-restraints excluded: chain C residue 2069 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 29 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 200 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 269 GLN A 352 GLN A 399 GLN A 536 HIS ** A 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 HIS ** C 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 GLN C 736 ASN C1053 GLN C1176 HIS ** C1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1599 HIS C1686 HIS C1723 ASN C1749 HIS ** C1870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.070578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.061605 restraints weight = 50656.060| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.98 r_work: 0.2914 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 17216 Z= 0.213 Angle : 0.688 10.497 23350 Z= 0.351 Chirality : 0.042 0.309 2729 Planarity : 0.005 0.066 2982 Dihedral : 4.774 55.273 2332 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.26 % Rotamer: Outliers : 4.91 % Allowed : 19.01 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.18), residues: 2152 helix: 1.10 (0.14), residues: 1442 sheet: -0.77 (0.76), residues: 48 loop : -1.63 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1774 TYR 0.028 0.002 TYR C2092 PHE 0.032 0.002 PHE C1618 TRP 0.030 0.002 TRP A 315 HIS 0.007 0.002 HIS C1630 Details of bonding type rmsd covalent geometry : bond 0.00504 (17210) covalent geometry : angle 0.68503 (23343) SS BOND : bond 0.01318 ( 2) SS BOND : angle 4.09834 ( 4) hydrogen bonds : bond 0.05578 ( 1025) hydrogen bonds : angle 4.35847 ( 3015) metal coordination : bond 0.01125 ( 4) metal coordination : angle 3.44270 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 342 time to evaluate : 0.702 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: A 242 ASP cc_start: 0.8572 (m-30) cc_final: 0.8075 (m-30) REVERT: A 245 GLN cc_start: 0.7869 (pp30) cc_final: 0.7590 (pp30) REVERT: A 272 LYS cc_start: 0.9054 (mttt) cc_final: 0.8847 (mttt) REVERT: A 276 GLU cc_start: 0.8791 (pp20) cc_final: 0.8543 (pp20) REVERT: A 315 TRP cc_start: 0.8763 (m-10) cc_final: 0.8535 (m-10) REVERT: A 319 TYR cc_start: 0.8595 (t80) cc_final: 0.8325 (t80) REVERT: A 552 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7468 (mm-30) REVERT: A 649 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8176 (ttp-170) REVERT: A 663 ASP cc_start: 0.7395 (t0) cc_final: 0.7068 (t0) REVERT: A 699 ASN cc_start: 0.8631 (t0) cc_final: 0.8362 (t0) REVERT: A 937 ASN cc_start: 0.8704 (t0) cc_final: 0.8405 (t0) REVERT: A 961 LEU cc_start: 0.7423 (tp) cc_final: 0.7099 (tp) REVERT: A 963 GLN cc_start: 0.7111 (mm-40) cc_final: 0.6713 (mm-40) REVERT: A 1042 MET cc_start: 0.8723 (tpt) cc_final: 0.8425 (tpt) REVERT: B 333 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.6890 (m-30) REVERT: B 337 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8492 (tt) REVERT: B 338 ARG cc_start: 0.8876 (ttm-80) cc_final: 0.8480 (ttm110) REVERT: C 760 LYS cc_start: 0.8770 (pttt) cc_final: 0.8559 (mtmm) REVERT: C 1001 LEU cc_start: 0.8805 (tp) cc_final: 0.8571 (tt) REVERT: C 1230 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8468 (mm) REVERT: C 1696 GLN cc_start: 0.7287 (tm-30) cc_final: 0.7054 (tm-30) REVERT: C 1818 GLU cc_start: 0.8179 (pt0) cc_final: 0.7701 (pt0) REVERT: C 1875 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8064 (mm-30) REVERT: C 1880 LEU cc_start: 0.8330 (mp) cc_final: 0.7957 (mp) REVERT: C 2080 TRP cc_start: 0.8536 (t60) cc_final: 0.8276 (t60) REVERT: C 2106 ILE cc_start: 0.9064 (mp) cc_final: 0.8844 (mm) outliers start: 88 outliers final: 55 residues processed: 401 average time/residue: 0.1396 time to fit residues: 82.9179 Evaluate side-chains 381 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 322 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 649 ARG Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 TYR Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 576 TRP Chi-restraints excluded: chain C residue 679 GLN Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 954 MET Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1027 CYS Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1055 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain C residue 1228 THR Chi-restraints excluded: chain C residue 1230 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1583 VAL Chi-restraints excluded: chain C residue 1607 CYS Chi-restraints excluded: chain C residue 1697 GLU Chi-restraints excluded: chain C residue 1706 VAL Chi-restraints excluded: chain C residue 1738 SER Chi-restraints excluded: chain C residue 1741 ILE Chi-restraints excluded: chain C residue 1850 THR Chi-restraints excluded: chain C residue 1873 LEU Chi-restraints excluded: chain C residue 1970 SER Chi-restraints excluded: chain C residue 2016 LEU Chi-restraints excluded: chain C residue 2039 ASN Chi-restraints excluded: chain C residue 2046 VAL Chi-restraints excluded: chain C residue 2069 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 166 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 183 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 99 optimal weight: 0.1980 chunk 79 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 202 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS ** A 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 HIS ** C 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN C1176 HIS ** C1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1686 HIS C1749 HIS ** C1870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.071029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.062067 restraints weight = 50601.370| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.98 r_work: 0.2926 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17216 Z= 0.170 Angle : 0.645 10.760 23350 Z= 0.329 Chirality : 0.040 0.323 2729 Planarity : 0.005 0.065 2982 Dihedral : 4.712 54.680 2332 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.51 % Favored : 95.45 % Rotamer: Outliers : 4.07 % Allowed : 20.68 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2152 helix: 1.23 (0.14), residues: 1441 sheet: -0.59 (0.78), residues: 48 loop : -1.51 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 451 TYR 0.028 0.002 TYR C2092 PHE 0.021 0.002 PHE C1618 TRP 0.019 0.002 TRP A 315 HIS 0.006 0.001 HIS C1686 Details of bonding type rmsd covalent geometry : bond 0.00399 (17210) covalent geometry : angle 0.64139 (23343) SS BOND : bond 0.00496 ( 2) SS BOND : angle 4.56389 ( 4) hydrogen bonds : bond 0.04981 ( 1025) hydrogen bonds : angle 4.24538 ( 3015) metal coordination : bond 0.00760 ( 4) metal coordination : angle 2.81950 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 335 time to evaluate : 0.737 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: A 276 GLU cc_start: 0.8770 (pp20) cc_final: 0.8471 (pp20) REVERT: A 315 TRP cc_start: 0.8837 (m-10) cc_final: 0.8595 (m-10) REVERT: A 552 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 649 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8270 (ttp-170) REVERT: A 663 ASP cc_start: 0.7392 (t0) cc_final: 0.7083 (t0) REVERT: A 699 ASN cc_start: 0.8627 (t0) cc_final: 0.8376 (t0) REVERT: A 725 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8182 (mtp) REVERT: A 961 LEU cc_start: 0.7395 (tp) cc_final: 0.7099 (tp) REVERT: A 963 GLN cc_start: 0.7368 (mm-40) cc_final: 0.6989 (mm-40) REVERT: A 1042 MET cc_start: 0.8742 (tpt) cc_final: 0.8455 (tpt) REVERT: B 333 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.6851 (m-30) REVERT: B 337 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8481 (tt) REVERT: B 338 ARG cc_start: 0.8874 (ttm-80) cc_final: 0.8558 (ttm110) REVERT: B 418 LYS cc_start: 0.8829 (ttpp) cc_final: 0.8604 (ttpp) REVERT: C 760 LYS cc_start: 0.8767 (pttt) cc_final: 0.8512 (mtmm) REVERT: C 1230 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8379 (mm) REVERT: C 1696 GLN cc_start: 0.7208 (tm-30) cc_final: 0.6977 (tm-30) REVERT: C 1774 ARG cc_start: 0.8167 (mtp-110) cc_final: 0.7965 (mtp85) REVERT: C 1818 GLU cc_start: 0.8193 (pt0) cc_final: 0.7931 (pm20) REVERT: C 1875 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8050 (mm-30) REVERT: C 2080 TRP cc_start: 0.8557 (t60) cc_final: 0.8246 (t60) REVERT: C 2106 ILE cc_start: 0.9049 (mp) cc_final: 0.8811 (mm) outliers start: 73 outliers final: 53 residues processed: 382 average time/residue: 0.1470 time to fit residues: 82.7887 Evaluate side-chains 376 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 318 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 649 ARG Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 TYR Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 679 GLN Chi-restraints excluded: chain C residue 783 TYR Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 920 SER Chi-restraints excluded: chain C residue 1027 CYS Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1055 LEU Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain C residue 1228 THR Chi-restraints excluded: chain C residue 1230 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1573 THR Chi-restraints excluded: chain C residue 1583 VAL Chi-restraints excluded: chain C residue 1607 CYS Chi-restraints excluded: chain C residue 1738 SER Chi-restraints excluded: chain C residue 1741 ILE Chi-restraints excluded: chain C residue 1749 HIS Chi-restraints excluded: chain C residue 1825 LEU Chi-restraints excluded: chain C residue 1850 THR Chi-restraints excluded: chain C residue 1873 LEU Chi-restraints excluded: chain C residue 1970 SER Chi-restraints excluded: chain C residue 1988 VAL Chi-restraints excluded: chain C residue 2016 LEU Chi-restraints excluded: chain C residue 2039 ASN Chi-restraints excluded: chain C residue 2046 VAL Chi-restraints excluded: chain C residue 2117 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 205 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 153 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 198 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 536 HIS ** A 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 HIS ** C 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 GLN C 982 GLN C1053 GLN C1176 HIS ** C1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1686 HIS C1749 HIS ** C1870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.069764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.060829 restraints weight = 50564.600| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.96 r_work: 0.2896 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17216 Z= 0.212 Angle : 0.699 11.289 23350 Z= 0.355 Chirality : 0.042 0.358 2729 Planarity : 0.005 0.064 2982 Dihedral : 4.854 56.130 2332 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.02 % Favored : 94.93 % Rotamer: Outliers : 4.52 % Allowed : 20.96 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.18), residues: 2152 helix: 1.15 (0.14), residues: 1436 sheet: -0.35 (0.80), residues: 48 loop : -1.51 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1774 TYR 0.030 0.002 TYR C2092 PHE 0.024 0.002 PHE C1030 TRP 0.014 0.002 TRP A 315 HIS 0.007 0.001 HIS C1749 Details of bonding type rmsd covalent geometry : bond 0.00505 (17210) covalent geometry : angle 0.69449 (23343) SS BOND : bond 0.01000 ( 2) SS BOND : angle 5.22679 ( 4) hydrogen bonds : bond 0.05419 ( 1025) hydrogen bonds : angle 4.34565 ( 3015) metal coordination : bond 0.01131 ( 4) metal coordination : angle 3.28787 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 334 time to evaluate : 0.722 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: A 272 LYS cc_start: 0.8688 (pptt) cc_final: 0.8479 (pptt) REVERT: A 276 GLU cc_start: 0.8801 (pp20) cc_final: 0.8485 (pp20) REVERT: A 315 TRP cc_start: 0.8934 (m-10) cc_final: 0.8653 (m-10) REVERT: A 552 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7353 (mm-30) REVERT: A 649 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8253 (ttp-170) REVERT: A 651 ASP cc_start: 0.8317 (t70) cc_final: 0.8050 (t0) REVERT: A 663 ASP cc_start: 0.7380 (t0) cc_final: 0.7124 (t0) REVERT: A 699 ASN cc_start: 0.8636 (t0) cc_final: 0.8421 (t0) REVERT: A 725 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8168 (mtp) REVERT: A 937 ASN cc_start: 0.8658 (t0) cc_final: 0.8386 (t0) REVERT: A 961 LEU cc_start: 0.7612 (tp) cc_final: 0.7304 (tp) REVERT: A 963 GLN cc_start: 0.7362 (mm-40) cc_final: 0.7027 (mm-40) REVERT: A 1042 MET cc_start: 0.8740 (tpt) cc_final: 0.8436 (tpt) REVERT: B 333 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.6776 (m-30) REVERT: B 418 LYS cc_start: 0.8916 (ttpp) cc_final: 0.8694 (ttpp) REVERT: C 760 LYS cc_start: 0.8743 (pttt) cc_final: 0.8539 (mtmm) REVERT: C 807 LYS cc_start: 0.8769 (mmmm) cc_final: 0.8544 (mmtm) REVERT: C 936 GLU cc_start: 0.7731 (tt0) cc_final: 0.7505 (tt0) REVERT: C 1230 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8448 (mm) REVERT: C 1696 GLN cc_start: 0.7165 (tm-30) cc_final: 0.6921 (tm-30) REVERT: C 1774 ARG cc_start: 0.8276 (mtp-110) cc_final: 0.7954 (mtp85) REVERT: C 1875 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8061 (mm-30) REVERT: C 2080 TRP cc_start: 0.8547 (t60) cc_final: 0.8290 (t60) REVERT: C 2106 ILE cc_start: 0.9066 (mp) cc_final: 0.8851 (mm) outliers start: 81 outliers final: 62 residues processed: 392 average time/residue: 0.1541 time to fit residues: 88.8737 Evaluate side-chains 389 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 323 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 649 ARG Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 TYR Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 679 GLN Chi-restraints excluded: chain C residue 783 TYR Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 954 MET Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1027 CYS Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1055 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain C residue 1228 THR Chi-restraints excluded: chain C residue 1230 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1573 THR Chi-restraints excluded: chain C residue 1583 VAL Chi-restraints excluded: chain C residue 1607 CYS Chi-restraints excluded: chain C residue 1697 GLU Chi-restraints excluded: chain C residue 1706 VAL Chi-restraints excluded: chain C residue 1738 SER Chi-restraints excluded: chain C residue 1741 ILE Chi-restraints excluded: chain C residue 1850 THR Chi-restraints excluded: chain C residue 1873 LEU Chi-restraints excluded: chain C residue 1900 GLN Chi-restraints excluded: chain C residue 1970 SER Chi-restraints excluded: chain C residue 1988 VAL Chi-restraints excluded: chain C residue 2016 LEU Chi-restraints excluded: chain C residue 2039 ASN Chi-restraints excluded: chain C residue 2046 VAL Chi-restraints excluded: chain C residue 2061 LEU Chi-restraints excluded: chain C residue 2069 ILE Chi-restraints excluded: chain C residue 2117 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 199 optimal weight: 0.0070 chunk 85 optimal weight: 0.9990 chunk 112 optimal weight: 0.0670 chunk 192 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 773 GLN A 780 ASN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 HIS ** C 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN C1176 HIS ** C1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1599 HIS C1686 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.070893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.061928 restraints weight = 50550.671| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.97 r_work: 0.2924 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17216 Z= 0.159 Angle : 0.660 11.159 23350 Z= 0.335 Chirality : 0.040 0.309 2729 Planarity : 0.005 0.062 2982 Dihedral : 4.764 54.804 2332 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.26 % Rotamer: Outliers : 4.24 % Allowed : 22.63 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 2152 helix: 1.30 (0.14), residues: 1435 sheet: -0.00 (0.84), residues: 48 loop : -1.44 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 338 TYR 0.029 0.002 TYR C2104 PHE 0.018 0.002 PHE A 289 TRP 0.015 0.002 TRP C1292 HIS 0.005 0.001 HIS C1686 Details of bonding type rmsd covalent geometry : bond 0.00370 (17210) covalent geometry : angle 0.65633 (23343) SS BOND : bond 0.00537 ( 2) SS BOND : angle 4.49268 ( 4) hydrogen bonds : bond 0.04785 ( 1025) hydrogen bonds : angle 4.19325 ( 3015) metal coordination : bond 0.00634 ( 4) metal coordination : angle 2.68493 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 332 time to evaluate : 0.646 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: A 272 LYS cc_start: 0.8774 (pptt) cc_final: 0.8555 (pptt) REVERT: A 276 GLU cc_start: 0.8823 (pp20) cc_final: 0.8553 (pp20) REVERT: A 315 TRP cc_start: 0.8923 (m-10) cc_final: 0.8675 (m-10) REVERT: A 316 MET cc_start: 0.8753 (mmm) cc_final: 0.8321 (mpp) REVERT: A 552 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7374 (mm-30) REVERT: A 649 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8321 (ttp-170) REVERT: A 651 ASP cc_start: 0.8339 (t70) cc_final: 0.8058 (t0) REVERT: A 663 ASP cc_start: 0.7331 (t0) cc_final: 0.7078 (t0) REVERT: A 961 LEU cc_start: 0.7626 (tp) cc_final: 0.7308 (tp) REVERT: A 963 GLN cc_start: 0.7357 (mm-40) cc_final: 0.7098 (mm-40) REVERT: A 967 ARG cc_start: 0.8494 (mtm-85) cc_final: 0.8287 (mtp180) REVERT: A 1042 MET cc_start: 0.8759 (tpt) cc_final: 0.8468 (tpt) REVERT: B 333 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.6759 (m-30) REVERT: C 807 LYS cc_start: 0.8747 (mmmm) cc_final: 0.8532 (mmtm) REVERT: C 951 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8422 (mp) REVERT: C 1230 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8340 (mm) REVERT: C 1696 GLN cc_start: 0.7032 (tm-30) cc_final: 0.6761 (tm-30) REVERT: C 1875 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7988 (mm-30) REVERT: C 2080 TRP cc_start: 0.8508 (t60) cc_final: 0.8241 (t60) REVERT: C 2106 ILE cc_start: 0.9034 (mp) cc_final: 0.8803 (mm) outliers start: 76 outliers final: 60 residues processed: 385 average time/residue: 0.1579 time to fit residues: 89.0676 Evaluate side-chains 378 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 314 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 649 ARG Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 TYR Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 679 GLN Chi-restraints excluded: chain C residue 746 CYS Chi-restraints excluded: chain C residue 783 TYR Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1027 CYS Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1055 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain C residue 1228 THR Chi-restraints excluded: chain C residue 1230 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1573 THR Chi-restraints excluded: chain C residue 1583 VAL Chi-restraints excluded: chain C residue 1607 CYS Chi-restraints excluded: chain C residue 1686 HIS Chi-restraints excluded: chain C residue 1697 GLU Chi-restraints excluded: chain C residue 1706 VAL Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1738 SER Chi-restraints excluded: chain C residue 1850 THR Chi-restraints excluded: chain C residue 1873 LEU Chi-restraints excluded: chain C residue 1970 SER Chi-restraints excluded: chain C residue 1988 VAL Chi-restraints excluded: chain C residue 2016 LEU Chi-restraints excluded: chain C residue 2039 ASN Chi-restraints excluded: chain C residue 2046 VAL Chi-restraints excluded: chain C residue 2069 ILE Chi-restraints excluded: chain C residue 2117 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 20 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 199 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 HIS ** C 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 GLN C1053 GLN C1176 HIS ** C1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1686 HIS ** C1855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.070503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.061580 restraints weight = 50875.898| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.97 r_work: 0.2915 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17216 Z= 0.175 Angle : 0.691 12.304 23350 Z= 0.350 Chirality : 0.041 0.347 2729 Planarity : 0.005 0.063 2982 Dihedral : 4.784 55.426 2332 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.97 % Favored : 94.98 % Rotamer: Outliers : 4.68 % Allowed : 23.02 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.18), residues: 2152 helix: 1.31 (0.14), residues: 1434 sheet: -0.05 (0.81), residues: 48 loop : -1.44 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 954 TYR 0.025 0.002 TYR C2092 PHE 0.018 0.002 PHE C1030 TRP 0.013 0.002 TRP C 683 HIS 0.010 0.001 HIS C1686 Details of bonding type rmsd covalent geometry : bond 0.00412 (17210) covalent geometry : angle 0.68661 (23343) SS BOND : bond 0.00407 ( 2) SS BOND : angle 5.68369 ( 4) hydrogen bonds : bond 0.04912 ( 1025) hydrogen bonds : angle 4.23730 ( 3015) metal coordination : bond 0.00802 ( 4) metal coordination : angle 2.80823 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 322 time to evaluate : 0.861 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: A 276 GLU cc_start: 0.8845 (pp20) cc_final: 0.8576 (pp20) REVERT: A 315 TRP cc_start: 0.8959 (m-10) cc_final: 0.8701 (m-10) REVERT: A 316 MET cc_start: 0.8765 (mmm) cc_final: 0.8345 (mpp) REVERT: A 365 GLU cc_start: 0.8662 (tp30) cc_final: 0.8456 (tp30) REVERT: A 552 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7381 (mm-30) REVERT: A 651 ASP cc_start: 0.8367 (t70) cc_final: 0.8096 (t0) REVERT: A 663 ASP cc_start: 0.7340 (t0) cc_final: 0.7085 (t0) REVERT: A 1041 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7585 (tt) REVERT: A 1042 MET cc_start: 0.8751 (tpt) cc_final: 0.8048 (tpt) REVERT: B 333 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6629 (m-30) REVERT: B 349 THR cc_start: 0.8502 (m) cc_final: 0.8254 (p) REVERT: C 807 LYS cc_start: 0.8725 (mmmm) cc_final: 0.8516 (mmtm) REVERT: C 911 TYR cc_start: 0.7167 (OUTLIER) cc_final: 0.6829 (t80) REVERT: C 1230 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8370 (mm) REVERT: C 1696 GLN cc_start: 0.6974 (tm-30) cc_final: 0.6700 (tm-30) REVERT: C 1774 ARG cc_start: 0.8116 (mtp180) cc_final: 0.7846 (mtp85) REVERT: C 1875 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8071 (mm-30) REVERT: C 1900 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7614 (pm20) REVERT: C 2080 TRP cc_start: 0.8461 (t60) cc_final: 0.8251 (t60) REVERT: C 2106 ILE cc_start: 0.9038 (mp) cc_final: 0.8822 (mm) outliers start: 84 outliers final: 70 residues processed: 378 average time/residue: 0.1578 time to fit residues: 87.0249 Evaluate side-chains 391 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 316 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 TYR Chi-restraints excluded: chain A residue 929 GLU Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 679 GLN Chi-restraints excluded: chain C residue 746 CYS Chi-restraints excluded: chain C residue 760 LYS Chi-restraints excluded: chain C residue 783 TYR Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 911 TYR Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 954 MET Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1027 CYS Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1055 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain C residue 1228 THR Chi-restraints excluded: chain C residue 1230 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1573 THR Chi-restraints excluded: chain C residue 1583 VAL Chi-restraints excluded: chain C residue 1607 CYS Chi-restraints excluded: chain C residue 1697 GLU Chi-restraints excluded: chain C residue 1706 VAL Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1738 SER Chi-restraints excluded: chain C residue 1741 ILE Chi-restraints excluded: chain C residue 1749 HIS Chi-restraints excluded: chain C residue 1850 THR Chi-restraints excluded: chain C residue 1900 GLN Chi-restraints excluded: chain C residue 1970 SER Chi-restraints excluded: chain C residue 1988 VAL Chi-restraints excluded: chain C residue 2016 LEU Chi-restraints excluded: chain C residue 2036 VAL Chi-restraints excluded: chain C residue 2039 ASN Chi-restraints excluded: chain C residue 2045 ILE Chi-restraints excluded: chain C residue 2046 VAL Chi-restraints excluded: chain C residue 2069 ILE Chi-restraints excluded: chain C residue 2117 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 3 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 213 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 198 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN A 934 ASN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN ** C1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1686 HIS ** C1855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.070204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.061292 restraints weight = 50566.299| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.97 r_work: 0.2909 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17216 Z= 0.185 Angle : 0.711 12.483 23350 Z= 0.364 Chirality : 0.041 0.335 2729 Planarity : 0.005 0.077 2982 Dihedral : 4.832 55.939 2332 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.02 % Favored : 94.93 % Rotamer: Outliers : 4.63 % Allowed : 23.36 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.18), residues: 2152 helix: 1.31 (0.14), residues: 1428 sheet: -0.13 (0.79), residues: 48 loop : -1.39 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 954 TYR 0.026 0.002 TYR C2092 PHE 0.020 0.002 PHE C1030 TRP 0.022 0.002 TRP C1292 HIS 0.006 0.001 HIS C1686 Details of bonding type rmsd covalent geometry : bond 0.00438 (17210) covalent geometry : angle 0.70615 (23343) SS BOND : bond 0.00472 ( 2) SS BOND : angle 5.54722 ( 4) hydrogen bonds : bond 0.05049 ( 1025) hydrogen bonds : angle 4.27162 ( 3015) metal coordination : bond 0.00887 ( 4) metal coordination : angle 2.92200 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 321 time to evaluate : 0.590 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: A 272 LYS cc_start: 0.9159 (pttt) cc_final: 0.8909 (mtmm) REVERT: A 276 GLU cc_start: 0.8866 (pp20) cc_final: 0.8609 (pp20) REVERT: A 315 TRP cc_start: 0.8959 (m-10) cc_final: 0.8658 (m-10) REVERT: A 316 MET cc_start: 0.8760 (mmm) cc_final: 0.8361 (mpp) REVERT: A 346 LYS cc_start: 0.8983 (mmtp) cc_final: 0.8655 (mmtp) REVERT: A 552 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7323 (mm-30) REVERT: A 651 ASP cc_start: 0.8364 (t70) cc_final: 0.8068 (t0) REVERT: A 663 ASP cc_start: 0.7326 (t0) cc_final: 0.7080 (t0) REVERT: A 890 MET cc_start: 0.8531 (mmm) cc_final: 0.8328 (mmt) REVERT: A 1041 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7568 (tt) REVERT: A 1042 MET cc_start: 0.8750 (tpt) cc_final: 0.8055 (tpt) REVERT: B 331 GLU cc_start: 0.7466 (tm-30) cc_final: 0.6709 (tm-30) REVERT: B 333 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6644 (m-30) REVERT: B 419 GLU cc_start: 0.8487 (tp30) cc_final: 0.8256 (tp30) REVERT: C 807 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8510 (mmtm) REVERT: C 936 GLU cc_start: 0.7689 (tt0) cc_final: 0.7475 (tt0) REVERT: C 951 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8449 (mp) REVERT: C 1230 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8391 (mm) REVERT: C 1738 SER cc_start: 0.6249 (OUTLIER) cc_final: 0.5807 (p) REVERT: C 1774 ARG cc_start: 0.8168 (mtp180) cc_final: 0.7917 (mtp85) REVERT: C 1818 GLU cc_start: 0.8360 (pt0) cc_final: 0.8160 (mt-10) REVERT: C 1875 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8150 (mm-30) REVERT: C 1879 ARG cc_start: 0.8076 (mtp180) cc_final: 0.7508 (tpt90) REVERT: C 2080 TRP cc_start: 0.8447 (t60) cc_final: 0.8246 (t60) REVERT: C 2106 ILE cc_start: 0.9072 (mp) cc_final: 0.8842 (mm) outliers start: 83 outliers final: 71 residues processed: 379 average time/residue: 0.1547 time to fit residues: 86.1357 Evaluate side-chains 381 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 305 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 TYR Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 679 GLN Chi-restraints excluded: chain C residue 746 CYS Chi-restraints excluded: chain C residue 783 TYR Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 911 TYR Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 954 MET Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1027 CYS Chi-restraints excluded: chain C residue 1033 LEU Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1055 LEU Chi-restraints excluded: chain C residue 1170 VAL Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain C residue 1228 THR Chi-restraints excluded: chain C residue 1230 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1573 THR Chi-restraints excluded: chain C residue 1577 ILE Chi-restraints excluded: chain C residue 1583 VAL Chi-restraints excluded: chain C residue 1607 CYS Chi-restraints excluded: chain C residue 1697 GLU Chi-restraints excluded: chain C residue 1706 VAL Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1738 SER Chi-restraints excluded: chain C residue 1741 ILE Chi-restraints excluded: chain C residue 1749 HIS Chi-restraints excluded: chain C residue 1850 THR Chi-restraints excluded: chain C residue 1873 LEU Chi-restraints excluded: chain C residue 1900 GLN Chi-restraints excluded: chain C residue 1970 SER Chi-restraints excluded: chain C residue 1988 VAL Chi-restraints excluded: chain C residue 2016 LEU Chi-restraints excluded: chain C residue 2036 VAL Chi-restraints excluded: chain C residue 2039 ASN Chi-restraints excluded: chain C residue 2045 ILE Chi-restraints excluded: chain C residue 2046 VAL Chi-restraints excluded: chain C residue 2069 ILE Chi-restraints excluded: chain C residue 2117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 43 optimal weight: 0.0970 chunk 101 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 192 optimal weight: 0.3980 chunk 113 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 191 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 176 optimal weight: 0.9990 chunk 147 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS ** A 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 GLN C1053 GLN C1208 HIS C1686 HIS ** C1855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1995 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.071526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.062620 restraints weight = 50622.847| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.98 r_work: 0.2942 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17216 Z= 0.154 Angle : 0.709 13.099 23350 Z= 0.363 Chirality : 0.040 0.308 2729 Planarity : 0.005 0.069 2982 Dihedral : 4.741 54.283 2332 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.37 % Favored : 95.59 % Rotamer: Outliers : 3.90 % Allowed : 24.41 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 2152 helix: 1.34 (0.14), residues: 1439 sheet: 0.07 (0.80), residues: 48 loop : -1.46 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 338 TYR 0.024 0.002 TYR C2092 PHE 0.016 0.001 PHE A 289 TRP 0.017 0.002 TRP A 315 HIS 0.006 0.001 HIS C1686 Details of bonding type rmsd covalent geometry : bond 0.00355 (17210) covalent geometry : angle 0.70554 (23343) SS BOND : bond 0.00374 ( 2) SS BOND : angle 5.05117 ( 4) hydrogen bonds : bond 0.04544 ( 1025) hydrogen bonds : angle 4.21815 ( 3015) metal coordination : bond 0.00449 ( 4) metal coordination : angle 2.32940 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4304 Ramachandran restraints generated. 2152 Oldfield, 0 Emsley, 2152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 322 time to evaluate : 0.708 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: A 272 LYS cc_start: 0.9175 (pttt) cc_final: 0.8902 (mtmm) REVERT: A 276 GLU cc_start: 0.8920 (pp20) cc_final: 0.8668 (pp20) REVERT: A 315 TRP cc_start: 0.8997 (m-10) cc_final: 0.8665 (m-10) REVERT: A 316 MET cc_start: 0.8775 (mmm) cc_final: 0.8305 (mpp) REVERT: A 552 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7310 (mm-30) REVERT: A 651 ASP cc_start: 0.8415 (t70) cc_final: 0.8103 (t0) REVERT: A 663 ASP cc_start: 0.7297 (t0) cc_final: 0.7043 (t0) REVERT: A 890 MET cc_start: 0.8517 (mmm) cc_final: 0.8252 (mmt) REVERT: A 959 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8412 (t80) REVERT: A 1041 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7562 (tt) REVERT: A 1042 MET cc_start: 0.8766 (tpt) cc_final: 0.8084 (tpt) REVERT: B 331 GLU cc_start: 0.7543 (tm-30) cc_final: 0.6773 (tm-30) REVERT: B 333 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.6810 (m-30) REVERT: B 419 GLU cc_start: 0.8462 (tp30) cc_final: 0.8261 (tp30) REVERT: C 911 TYR cc_start: 0.7067 (OUTLIER) cc_final: 0.6781 (t80) REVERT: C 951 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8362 (mp) REVERT: C 1140 LEU cc_start: 0.9111 (mp) cc_final: 0.8848 (mp) REVERT: C 1230 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8316 (mm) REVERT: C 1738 SER cc_start: 0.6371 (OUTLIER) cc_final: 0.6095 (p) REVERT: C 1875 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8102 (mm-30) REVERT: C 1879 ARG cc_start: 0.8005 (mtp180) cc_final: 0.7550 (tpt90) REVERT: C 2106 ILE cc_start: 0.9023 (mp) cc_final: 0.8766 (mm) outliers start: 70 outliers final: 53 residues processed: 369 average time/residue: 0.1522 time to fit residues: 83.0615 Evaluate side-chains 373 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 313 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 636 TYR Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 863 ASN Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 896 TYR Chi-restraints excluded: chain A residue 959 PHE Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 425 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 679 GLN Chi-restraints excluded: chain C residue 746 CYS Chi-restraints excluded: chain C residue 760 LYS Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 908 VAL Chi-restraints excluded: chain C residue 911 TYR Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1027 CYS Chi-restraints excluded: chain C residue 1045 ASP Chi-restraints excluded: chain C residue 1055 LEU Chi-restraints excluded: chain C residue 1210 THR Chi-restraints excluded: chain C residue 1228 THR Chi-restraints excluded: chain C residue 1230 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1573 THR Chi-restraints excluded: chain C residue 1583 VAL Chi-restraints excluded: chain C residue 1607 CYS Chi-restraints excluded: chain C residue 1697 GLU Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1738 SER Chi-restraints excluded: chain C residue 1741 ILE Chi-restraints excluded: chain C residue 1749 HIS Chi-restraints excluded: chain C residue 1850 THR Chi-restraints excluded: chain C residue 1873 LEU Chi-restraints excluded: chain C residue 1970 SER Chi-restraints excluded: chain C residue 1988 VAL Chi-restraints excluded: chain C residue 2016 LEU Chi-restraints excluded: chain C residue 2036 VAL Chi-restraints excluded: chain C residue 2039 ASN Chi-restraints excluded: chain C residue 2045 ILE Chi-restraints excluded: chain C residue 2046 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 47 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 174 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 182 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 GLN C1053 GLN C1686 HIS ** C1855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.070567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.061684 restraints weight = 50602.535| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.97 r_work: 0.2918 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17216 Z= 0.183 Angle : 0.734 12.997 23350 Z= 0.377 Chirality : 0.041 0.322 2729 Planarity : 0.005 0.076 2982 Dihedral : 4.815 55.332 2332 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.79 % Favored : 95.17 % Rotamer: Outliers : 3.68 % Allowed : 24.58 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 2152 helix: 1.31 (0.14), residues: 1425 sheet: 0.09 (0.80), residues: 48 loop : -1.47 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C1774 TYR 0.028 0.002 TYR C2092 PHE 0.018 0.002 PHE C1030 TRP 0.045 0.002 TRP C2080 HIS 0.006 0.001 HIS C1686 Details of bonding type rmsd covalent geometry : bond 0.00431 (17210) covalent geometry : angle 0.73026 (23343) SS BOND : bond 0.00431 ( 2) SS BOND : angle 5.26498 ( 4) hydrogen bonds : bond 0.04935 ( 1025) hydrogen bonds : angle 4.28093 ( 3015) metal coordination : bond 0.00806 ( 4) metal coordination : angle 2.75351 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4418.98 seconds wall clock time: 76 minutes 31.92 seconds (4591.92 seconds total)