Starting phenix.real_space_refine on Fri Sep 11 13:11:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xnx_67062/09_2026/9xnx_67062.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xnx_67062/09_2026/9xnx_67062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xnx_67062/09_2026/9xnx_67062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xnx_67062/09_2026/9xnx_67062.map" model { file = "/net/cci-nas-00/data/ceres_data/9xnx_67062/09_2026/9xnx_67062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xnx_67062/09_2026/9xnx_67062.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 5797 2.51 5 N 1464 2.21 5 O 1820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9125 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 8804 Classifications: {'peptide': 1147} Link IDs: {'PTRANS': 42, 'TRANS': 1104} Chain breaks: 8 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 204 Unusual residues: {'NAG': 12, 'PAM': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 1.94, per 1000 atoms: 0.21 Number of scatterers: 9125 At special positions: 0 Unit cell: (108.81, 119.04, 164.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1820 8.00 N 1464 7.00 C 5797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 202 " distance=2.02 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.03 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.03 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " distance=2.03 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 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1401 " - " ASN A 324 " " NAG A1402 " - " ASN A 216 " " NAG A1403 " - " ASN A 514 " " NAG A1404 " - " ASN A 726 " " NAG A1405 " - " ASN A 781 " " NAG A1406 " - " ASN A 743 " " NAG A1407 " - " ASN A 787 " " NAG A1408 " - " ASN A 873 " " NAG A1409 " - " ASN A1009 " " NAG A1410 " - " ASN A1232 " " NAG A1411 " - " ASN A 344 " " NAG A1412 " - " ASN A 351 " " NAG B 1 " - " ASN A 264 " " NAG C 1 " - " ASN A 688 " " NAG D 1 " - " ASN A 425 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 335.8 milliseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 19 sheets defined 20.9% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.760A pdb=" N GLY A 224 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE A 225 " --> pdb=" O GLU A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 225' Processing helix chain 'A' and resid 325 through 329 removed outlier: 3.603A pdb=" N VAL A 328 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.697A pdb=" N ALA A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 Processing helix chain 'A' and resid 807 through 813 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 828 through 852 removed outlier: 3.950A pdb=" N ILE A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 860 Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 917 through 921 removed outlier: 3.702A pdb=" N SER A 921 " --> pdb=" O LYS A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 936 Processing helix chain 'A' and resid 946 through 960 Processing helix chain 'A' and resid 973 through 986 removed outlier: 3.808A pdb=" N ALA A 977 " --> pdb=" O PRO A 973 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR A 984 " --> pdb=" O ALA A 980 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1016 removed outlier: 3.642A pdb=" N GLU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A1011 " --> pdb=" O ILE A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1044 Processing helix chain 'A' and resid 1045 through 1054 removed outlier: 4.442A pdb=" N LEU A1049 " --> pdb=" O GLN A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1074 Processing helix chain 'A' and resid 1075 through 1123 removed outlier: 3.704A pdb=" N ASP A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A1085 " --> pdb=" O VAL A1081 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A1086 " --> pdb=" O GLN A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'A' and resid 1234 through 1236 No H-bonds generated for 'chain 'A' and resid 1234 through 1236' Processing helix chain 'A' and resid 1237 through 1242 removed outlier: 3.799A pdb=" N VAL A1241 " --> pdb=" O GLN A1237 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 25 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.590A pdb=" N VAL A 47 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 184 removed outlier: 3.570A pdb=" N GLY A 165 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA5, first strand: chain 'A' and resid 106 through 111 removed outlier: 6.900A pdb=" N ILE A 125 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 106 through 111 Processing sheet with id=AA7, first strand: chain 'A' and resid 270 through 288 removed outlier: 5.541A pdb=" N LYS A 272 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL A 453 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL A 274 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE A 451 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASN A 276 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA A 449 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 447 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER A 443 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU A 284 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 441 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA A 286 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TRP A 439 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 406 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 270 through 288 removed outlier: 5.541A pdb=" N LYS A 272 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL A 453 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL A 274 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE A 451 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASN A 276 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA A 449 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 447 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER A 443 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU A 284 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 441 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA A 286 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TRP A 439 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLU A 452 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 457 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 296 through 298 removed outlier: 6.844A pdb=" N HIS A 338 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL A 422 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL A 336 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 296 through 298 removed outlier: 6.844A pdb=" N HIS A 338 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL A 422 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL A 336 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N CYS A 373 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 483 through 488 removed outlier: 3.635A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 738 " --> pdb=" O SER A 727 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 499 through 502 removed outlier: 4.683A pdb=" N VAL A 694 " --> pdb=" O THR A 666 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 526 through 536 removed outlier: 6.271A pdb=" N ASN A 528 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 522 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N SER A 520 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 532 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER A 518 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR A 534 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A 516 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE A 536 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASN A 514 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A 587 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY A 625 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE A 585 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU A 627 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N LEU A 583 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 526 through 536 removed outlier: 6.271A pdb=" N ASN A 528 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 522 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N SER A 520 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 532 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER A 518 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N THR A 534 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR A 516 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE A 536 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASN A 514 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LYS A 614 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY A 605 " --> pdb=" O LYS A 614 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR A 616 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 749 through 750 Processing sheet with id=AB7, first strand: chain 'A' and resid 780 through 798 removed outlier: 3.528A pdb=" N GLY A 780 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE A 788 " --> pdb=" O PRO A1160 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET A 790 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU A1158 " --> pdb=" O MET A 790 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A 792 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR A1156 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU A1154 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR A 796 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU A1152 " --> pdb=" O TYR A 796 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLN A 798 " --> pdb=" O GLY A1150 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY A1150 " --> pdb=" O GLN A 798 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A1141 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU A1158 " --> pdb=" O HIS A1139 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N HIS A1139 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB9, first strand: chain 'A' and resid 1220 through 1223 removed outlier: 4.246A pdb=" N ALA A1179 " --> pdb=" O ILE A1223 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A1178 " --> pdb=" O VAL A1174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1187 through 1190 350 hydrogen bonds defined for protein. 969 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: 2.13 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2871 1.34 - 1.46: 2380 1.46 - 1.58: 4007 1.58 - 1.71: 0 1.71 - 1.83: 56 Bond restraints: 9314 Sorted by residual: bond pdb=" C ALA A 43 " pdb=" N PRO A 44 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.40e+00 bond pdb=" C VAL A 748 " pdb=" O VAL A 748 " ideal model delta sigma weight residual 1.233 1.243 -0.011 1.02e-02 9.61e+03 1.08e+00 bond pdb=" CB CYS A 202 " pdb=" SG CYS A 202 " ideal model delta sigma weight residual 1.808 1.774 0.034 3.30e-02 9.18e+02 1.04e+00 bond pdb=" CA THR A 456 " pdb=" CB THR A 456 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 1.00e+00 bond pdb=" CB ARG A 981 " pdb=" CG ARG A 981 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.33e-01 ... (remaining 9309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 12519 2.32 - 4.65: 134 4.65 - 6.97: 7 6.97 - 9.29: 1 9.29 - 11.62: 1 Bond angle restraints: 12662 Sorted by residual: angle pdb=" C2 NAG A1410 " pdb=" N2 NAG A1410 " pdb=" C7 NAG A1410 " ideal model delta sigma weight residual 124.56 136.18 -11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" C GLY A 455 " pdb=" N THR A 456 " pdb=" CA THR A 456 " ideal model delta sigma weight residual 121.54 126.99 -5.45 1.91e+00 2.74e-01 8.14e+00 angle pdb=" C ASP A 466 " pdb=" CA ASP A 466 " pdb=" CB ASP A 466 " ideal model delta sigma weight residual 109.37 113.77 -4.40 1.59e+00 3.96e-01 7.67e+00 angle pdb=" C THR A 863 " pdb=" N ILE A 864 " pdb=" CA ILE A 864 " ideal model delta sigma weight residual 121.97 117.65 4.32 1.80e+00 3.09e-01 5.75e+00 angle pdb=" C8 NAG A1410 " pdb=" C7 NAG A1410 " pdb=" N2 NAG A1410 " ideal model delta sigma weight residual 115.06 121.58 -6.52 3.00e+00 1.11e-01 4.73e+00 ... (remaining 12657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.00: 5525 24.00 - 47.99: 208 47.99 - 71.99: 27 71.99 - 95.98: 6 95.98 - 119.98: 3 Dihedral angle restraints: 5769 sinusoidal: 2450 harmonic: 3319 Sorted by residual: dihedral pdb=" CB CYS A 649 " pdb=" SG CYS A 649 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -16.52 -69.48 1 1.00e+01 1.00e-02 6.24e+01 dihedral pdb=" SG CYS A 349 " pdb=" CB CYS A 373 " pdb=" SG CYS A 373 " pdb=" CA CYS A 373 " ideal model delta sinusoidal sigma weight residual -73.00 2.58 -75.58 1 2.00e+01 2.50e-03 1.80e+01 dihedral pdb=" CA PHE A 91 " pdb=" C PHE A 91 " pdb=" N GLU A 92 " pdb=" CA GLU A 92 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 5766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1292 0.062 - 0.123: 196 0.123 - 0.185: 23 0.185 - 0.246: 0 0.246 - 0.308: 4 Chirality restraints: 1515 Sorted by residual: chirality pdb=" C1 NAG A1409 " pdb=" ND2 ASN A1009 " pdb=" C2 NAG A1409 " pdb=" O5 NAG A1409 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C2 NAG A1410 " pdb=" C1 NAG A1410 " pdb=" C3 NAG A1410 " pdb=" N2 NAG A1410 " both_signs ideal model delta sigma weight residual False -2.49 -2.19 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C1 NAG A1404 " pdb=" ND2 ASN A 726 " pdb=" C2 NAG A1404 " pdb=" O5 NAG A1404 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1512 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 466 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO A 467 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 467 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 467 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 98 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 99 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 731 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO A 732 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 732 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 732 " -0.022 5.00e-02 4.00e+02 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 5237 3.04 - 3.50: 8466 3.50 - 3.97: 14657 3.97 - 4.43: 16668 4.43 - 4.90: 26851 Nonbonded interactions: 71879 Sorted by model distance: nonbonded pdb=" C3 MAN B 5 " pdb=" O5 MAN B 5 " model vdw 2.569 2.776 nonbonded pdb=" O ARG A1183 " pdb=" CA GLU A1184 " model vdw 2.576 2.776 nonbonded pdb=" O5 MAN B 4 " pdb=" O6 MAN B 4 " model vdw 2.619 2.432 nonbonded pdb=" N LYS A 633 " pdb=" O LYS A 633 " model vdw 2.626 2.496 nonbonded pdb=" O2 BMA B 3 " pdb=" O3 BMA B 3 " model vdw 2.631 2.432 ... (remaining 71874 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.030 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 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 : 0.003 0.034 9351 Z= 0.124 Angle : 0.609 11.617 12757 Z= 0.311 Chirality : 0.047 0.308 1515 Planarity : 0.005 0.046 1602 Dihedral : 12.472 119.976 3595 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.25), residues: 1129 helix: 0.12 (0.35), residues: 205 sheet: -0.20 (0.33), residues: 269 loop : -1.18 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 919 TYR 0.015 0.001 TYR A 181 PHE 0.014 0.001 PHE A 615 TRP 0.004 0.001 TRP A 65 HIS 0.005 0.001 HIS A 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 9314) covalent geometry : angle 0.59496 / 0.31 (12662) SS BOND : bond 0.00270 / 0.15 ( 16) SS BOND : angle 1.31138 / 0.85 ( 32) hydrogen bonds : bond 0.18474 / 11.54 ( 319) hydrogen bonds : angle 8.82082 / 6.21 ( 969) link_ALPHA1-3 : bond 0.00737 / 0.39 ( 1) link_ALPHA1-3 : angle 1.30793 / 0.72 ( 3) link_ALPHA1-6 : bond 0.00711 / 0.37 ( 1) link_ALPHA1-6 : angle 1.25700 / 0.69 ( 3) link_BETA1-4 : bond 0.00268 / 0.14 ( 4) link_BETA1-4 : angle 1.75535 / 1.11 ( 12) link_NAG-ASN : bond 0.00369 / 0.25 ( 15) link_NAG-ASN : angle 1.79886 / 1.40 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.7724 (tt) cc_final: 0.7382 (tm) REVERT: A 151 ASN cc_start: 0.7874 (t0) cc_final: 0.7498 (t0) REVERT: A 157 HIS cc_start: 0.6602 (t70) cc_final: 0.6323 (t70) REVERT: A 226 SER cc_start: 0.7830 (m) cc_final: 0.7424 (t) REVERT: A 542 PHE cc_start: 0.8613 (t80) cc_final: 0.8365 (t80) REVERT: A 569 ASP cc_start: 0.7536 (t0) cc_final: 0.7183 (t0) REVERT: A 617 SER cc_start: 0.8247 (m) cc_final: 0.7978 (p) REVERT: A 682 GLN cc_start: 0.7903 (mp10) cc_final: 0.7427 (mp10) REVERT: A 701 SER cc_start: 0.8318 (t) cc_final: 0.8070 (p) REVERT: A 774 ILE cc_start: 0.8658 (mm) cc_final: 0.8448 (mp) outliers start: 0 outliers final: 1 residues processed: 185 average time/residue: 0.4445 time to fit residues: 89.4146 Evaluate side-chains 171 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 HIS A 270 HIS A 295 GLN A 445 ASN A 556 ASN A 577 GLN A1055 GLN A1126 GLN A1149 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.124753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.107054 restraints weight = 12454.523| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.88 r_work: 0.3253 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9351 Z= 0.158 Angle : 0.579 9.813 12757 Z= 0.295 Chirality : 0.045 0.333 1515 Planarity : 0.004 0.044 1602 Dihedral : 7.731 104.326 1688 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.03 % Allowed : 7.00 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.25), residues: 1129 helix: 0.90 (0.37), residues: 205 sheet: -0.33 (0.31), residues: 307 loop : -1.09 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1085 TYR 0.010 0.001 TYR A 181 PHE 0.014 0.001 PHE A 615 TRP 0.004 0.001 TRP A 259 HIS 0.003 0.001 HIS A 951 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 9314) covalent geometry : angle 0.55647 / 0.29 (12662) SS BOND : bond 0.00648 / 0.39 ( 16) SS BOND : angle 2.18382 / 1.56 ( 32) hydrogen bonds : bond 0.04289 / 2.68 ( 319) hydrogen bonds : angle 6.14427 / 4.38 ( 969) link_ALPHA1-3 : bond 0.00453 / 0.24 ( 1) link_ALPHA1-3 : angle 1.53202 / 0.85 ( 3) link_ALPHA1-6 : bond 0.00962 / 0.51 ( 1) link_ALPHA1-6 : angle 2.01411 / 1.10 ( 3) link_BETA1-4 : bond 0.00138 / 0.07 ( 4) link_BETA1-4 : angle 1.74781 / 1.04 ( 12) link_NAG-ASN : bond 0.00333 / 0.23 ( 15) link_NAG-ASN : angle 1.80629 / 1.37 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 HIS cc_start: 0.6219 (m-70) cc_final: 0.5987 (m170) REVERT: A 109 LEU cc_start: 0.7779 (tt) cc_final: 0.7420 (tm) REVERT: A 126 CYS cc_start: 0.5709 (OUTLIER) cc_final: 0.5296 (m) REVERT: A 157 HIS cc_start: 0.6638 (t70) cc_final: 0.6372 (t70) REVERT: A 191 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7181 (tpp-160) REVERT: A 226 SER cc_start: 0.7976 (m) cc_final: 0.7529 (t) REVERT: A 347 PHE cc_start: 0.8060 (t80) cc_final: 0.7616 (t80) REVERT: A 383 THR cc_start: 0.8233 (m) cc_final: 0.8020 (t) REVERT: A 569 ASP cc_start: 0.7582 (t0) cc_final: 0.7340 (t0) REVERT: A 682 GLN cc_start: 0.7989 (mp10) cc_final: 0.7465 (mp10) REVERT: A 701 SER cc_start: 0.8344 (t) cc_final: 0.8107 (p) REVERT: A 774 ILE cc_start: 0.8659 (mm) cc_final: 0.8442 (mp) outliers start: 20 outliers final: 8 residues processed: 184 average time/residue: 0.4574 time to fit residues: 91.5660 Evaluate side-chains 176 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 624 LYS Chi-restraints excluded: chain A residue 779 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 58 optimal weight: 0.0970 chunk 36 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 445 ASN A 577 GLN A1045 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106584 restraints weight = 12406.505| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.87 r_work: 0.3246 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9351 Z= 0.163 Angle : 0.621 22.258 12757 Z= 0.311 Chirality : 0.046 0.418 1515 Planarity : 0.004 0.043 1602 Dihedral : 6.979 94.943 1685 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.13 % Allowed : 8.62 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.25), residues: 1129 helix: 1.03 (0.37), residues: 211 sheet: -0.14 (0.31), residues: 294 loop : -1.06 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1085 TYR 0.009 0.001 TYR A 676 PHE 0.015 0.001 PHE A 91 TRP 0.004 0.001 TRP A 259 HIS 0.003 0.001 HIS A1139 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 9314) covalent geometry : angle 0.59093 / 0.30 (12662) SS BOND : bond 0.00537 / 0.24 ( 16) SS BOND : angle 2.99465 / 2.15 ( 32) hydrogen bonds : bond 0.03859 / 2.46 ( 319) hydrogen bonds : angle 5.73537 / 4.11 ( 969) link_ALPHA1-3 : bond 0.00407 / 0.21 ( 1) link_ALPHA1-3 : angle 1.55169 / 0.86 ( 3) link_ALPHA1-6 : bond 0.01147 / 0.60 ( 1) link_ALPHA1-6 : angle 2.45915 / 1.34 ( 3) link_BETA1-4 : bond 0.00150 / 0.08 ( 4) link_BETA1-4 : angle 1.73894 / 1.03 ( 12) link_NAG-ASN : bond 0.00341 / 0.23 ( 15) link_NAG-ASN : angle 1.79703 / 1.34 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 109 LEU cc_start: 0.7801 (tt) cc_final: 0.7460 (tm) REVERT: A 157 HIS cc_start: 0.6655 (t70) cc_final: 0.6413 (t70) REVERT: A 213 TYR cc_start: 0.6683 (m-10) cc_final: 0.6415 (m-80) REVERT: A 226 SER cc_start: 0.7975 (m) cc_final: 0.7525 (t) REVERT: A 347 PHE cc_start: 0.8010 (t80) cc_final: 0.7633 (t80) REVERT: A 569 ASP cc_start: 0.7564 (t0) cc_final: 0.7324 (t0) REVERT: A 651 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8311 (ttmt) REVERT: A 701 SER cc_start: 0.8345 (t) cc_final: 0.8120 (p) REVERT: A 774 ILE cc_start: 0.8676 (mm) cc_final: 0.8451 (mp) outliers start: 21 outliers final: 10 residues processed: 182 average time/residue: 0.4718 time to fit residues: 93.1526 Evaluate side-chains 182 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 62 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 42 optimal weight: 0.1980 chunk 25 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN A 270 HIS A1045 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105103 restraints weight = 12535.923| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.87 r_work: 0.3223 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 9351 Z= 0.212 Angle : 0.647 12.901 12757 Z= 0.328 Chirality : 0.048 0.352 1515 Planarity : 0.004 0.042 1602 Dihedral : 6.770 78.970 1685 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.94 % Allowed : 9.23 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.25), residues: 1129 helix: 1.03 (0.36), residues: 211 sheet: -0.46 (0.30), residues: 303 loop : -1.01 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 924 TYR 0.013 0.001 TYR A 213 PHE 0.019 0.002 PHE A 91 TRP 0.007 0.001 TRP A 439 HIS 0.006 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 ( 9314) covalent geometry : angle 0.61331 / 0.32 (12662) SS BOND : bond 0.00524 / 0.28 ( 16) SS BOND : angle 3.23046 / 2.31 ( 32) hydrogen bonds : bond 0.03894 / 2.50 ( 319) hydrogen bonds : angle 5.72002 / 4.16 ( 969) link_ALPHA1-3 : bond 0.00222 / 0.12 ( 1) link_ALPHA1-3 : angle 1.70547 / 0.95 ( 3) link_ALPHA1-6 : bond 0.01293 / 0.68 ( 1) link_ALPHA1-6 : angle 2.80821 / 1.51 ( 3) link_BETA1-4 : bond 0.00088 / 0.04 ( 4) link_BETA1-4 : angle 1.77209 / 1.02 ( 12) link_NAG-ASN : bond 0.00397 / 0.26 ( 15) link_NAG-ASN : angle 1.97079 / 1.49 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 126 CYS cc_start: 0.5730 (OUTLIER) cc_final: 0.5183 (m) REVERT: A 151 ASN cc_start: 0.7847 (t0) cc_final: 0.7615 (t0) REVERT: A 157 HIS cc_start: 0.6667 (t70) cc_final: 0.6431 (t70) REVERT: A 191 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7257 (tpp-160) REVERT: A 213 TYR cc_start: 0.6681 (m-10) cc_final: 0.6452 (m-80) REVERT: A 347 PHE cc_start: 0.8138 (t80) cc_final: 0.7772 (t80) REVERT: A 348 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8102 (m) REVERT: A 518 SER cc_start: 0.8245 (m) cc_final: 0.8018 (t) REVERT: A 651 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8317 (ttmt) REVERT: A 745 THR cc_start: 0.7731 (p) cc_final: 0.7520 (p) REVERT: A 774 ILE cc_start: 0.8678 (mm) cc_final: 0.8446 (mp) REVERT: A 1045 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7862 (mm110) outliers start: 29 outliers final: 16 residues processed: 192 average time/residue: 0.4766 time to fit residues: 99.0762 Evaluate side-chains 189 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 470 GLN Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1174 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 64 optimal weight: 0.6980 chunk 63 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 chunk 13 optimal weight: 0.4980 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN A 459 GLN A 979 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.122747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105224 restraints weight = 12449.662| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.87 r_work: 0.3224 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 9351 Z= 0.196 Angle : 0.632 11.118 12757 Z= 0.319 Chirality : 0.047 0.298 1515 Planarity : 0.004 0.040 1602 Dihedral : 6.376 53.210 1685 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.25 % Allowed : 10.34 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.25), residues: 1129 helix: 1.09 (0.36), residues: 212 sheet: -0.45 (0.30), residues: 296 loop : -1.02 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1183 TYR 0.014 0.001 TYR A 213 PHE 0.019 0.002 PHE A 91 TRP 0.007 0.001 TRP A 439 HIS 0.005 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 ( 9314) covalent geometry : angle 0.60079 / 0.31 (12662) SS BOND : bond 0.00549 / 0.31 ( 16) SS BOND : angle 3.00340 / 1.98 ( 32) hydrogen bonds : bond 0.03773 / 2.41 ( 319) hydrogen bonds : angle 5.56741 / 4.04 ( 969) link_ALPHA1-3 : bond 0.00341 / 0.18 ( 1) link_ALPHA1-3 : angle 1.67507 / 0.93 ( 3) link_ALPHA1-6 : bond 0.01534 / 0.81 ( 1) link_ALPHA1-6 : angle 2.69907 / 1.44 ( 3) link_BETA1-4 : bond 0.00092 / 0.05 ( 4) link_BETA1-4 : angle 1.71353 / 1.00 ( 12) link_NAG-ASN : bond 0.00357 / 0.23 ( 15) link_NAG-ASN : angle 1.96002 / 1.49 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.343 Fit side-chains REVERT: A 126 CYS cc_start: 0.5699 (OUTLIER) cc_final: 0.5227 (m) REVERT: A 157 HIS cc_start: 0.6667 (t70) cc_final: 0.6429 (t70) REVERT: A 191 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7295 (tpp-160) REVERT: A 213 TYR cc_start: 0.6827 (m-10) cc_final: 0.6595 (m-80) REVERT: A 347 PHE cc_start: 0.8106 (t80) cc_final: 0.7657 (t80) REVERT: A 348 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.8034 (m) REVERT: A 518 SER cc_start: 0.8264 (m) cc_final: 0.8041 (t) REVERT: A 651 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8300 (ttmt) REVERT: A 710 ASP cc_start: 0.8182 (m-30) cc_final: 0.7976 (m-30) REVERT: A 774 ILE cc_start: 0.8671 (mm) cc_final: 0.8440 (mp) REVERT: A 1039 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8104 (mm-40) outliers start: 32 outliers final: 18 residues processed: 184 average time/residue: 0.4897 time to fit residues: 97.4970 Evaluate side-chains 194 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 470 GLN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1174 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 44 optimal weight: 0.0000 chunk 98 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN A1045 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.123411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105927 restraints weight = 12523.848| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.88 r_work: 0.3233 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9351 Z= 0.156 Angle : 0.606 14.645 12757 Z= 0.307 Chirality : 0.046 0.357 1515 Planarity : 0.004 0.040 1602 Dihedral : 6.148 59.844 1685 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.14 % Allowed : 11.46 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.25), residues: 1129 helix: 1.20 (0.36), residues: 212 sheet: -0.43 (0.30), residues: 285 loop : -0.96 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1183 TYR 0.014 0.001 TYR A 213 PHE 0.018 0.001 PHE A 91 TRP 0.005 0.001 TRP A 439 HIS 0.007 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 9314) covalent geometry : angle 0.57808 / 0.30 (12662) SS BOND : bond 0.00657 / 0.33 ( 16) SS BOND : angle 2.83277 / 1.87 ( 32) hydrogen bonds : bond 0.03585 / 2.29 ( 319) hydrogen bonds : angle 5.42701 / 3.96 ( 969) link_ALPHA1-3 : bond 0.00474 / 0.25 ( 1) link_ALPHA1-3 : angle 1.58806 / 0.87 ( 3) link_ALPHA1-6 : bond 0.01069 / 0.56 ( 1) link_ALPHA1-6 : angle 1.77777 / 0.96 ( 3) link_BETA1-4 : bond 0.00153 / 0.08 ( 4) link_BETA1-4 : angle 1.61370 / 0.95 ( 12) link_NAG-ASN : bond 0.00341 / 0.23 ( 15) link_NAG-ASN : angle 1.85673 / 1.40 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.330 Fit side-chains REVERT: A 126 CYS cc_start: 0.5725 (OUTLIER) cc_final: 0.5246 (m) REVERT: A 157 HIS cc_start: 0.6663 (t70) cc_final: 0.6435 (t70) REVERT: A 191 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7159 (tpp-160) REVERT: A 213 TYR cc_start: 0.6941 (m-10) cc_final: 0.6614 (m-80) REVERT: A 322 ASN cc_start: 0.8439 (t0) cc_final: 0.8228 (t0) REVERT: A 347 PHE cc_start: 0.7970 (t80) cc_final: 0.7691 (t80) REVERT: A 348 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7858 (m) REVERT: A 518 SER cc_start: 0.8291 (m) cc_final: 0.8081 (t) REVERT: A 651 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8302 (ttmt) REVERT: A 682 GLN cc_start: 0.8045 (mp10) cc_final: 0.7671 (mp10) REVERT: A 774 ILE cc_start: 0.8677 (mm) cc_final: 0.8436 (mp) REVERT: A 1039 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8105 (mm-40) outliers start: 31 outliers final: 18 residues processed: 184 average time/residue: 0.5060 time to fit residues: 100.5048 Evaluate side-chains 193 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 624 LYS Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1174 VAL Chi-restraints excluded: chain A residue 1184 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 73 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 HIS A 445 ASN A 571 ASN A 577 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.121699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104391 restraints weight = 12485.138| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.85 r_work: 0.3208 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 9351 Z= 0.248 Angle : 0.656 11.704 12757 Z= 0.334 Chirality : 0.049 0.353 1515 Planarity : 0.004 0.042 1602 Dihedral : 6.349 59.279 1685 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.45 % Allowed : 11.66 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.24), residues: 1129 helix: 1.04 (0.36), residues: 212 sheet: -0.49 (0.30), residues: 289 loop : -1.05 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1183 TYR 0.021 0.002 TYR A 213 PHE 0.021 0.002 PHE A 91 TRP 0.010 0.002 TRP A 439 HIS 0.010 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.25 ( 9314) covalent geometry : angle 0.62372 / 0.32 (12662) SS BOND : bond 0.00620 / 0.35 ( 16) SS BOND : angle 3.07412 / 2.05 ( 32) hydrogen bonds : bond 0.03975 / 2.54 ( 319) hydrogen bonds : angle 5.51281 / 4.02 ( 969) link_ALPHA1-3 : bond 0.00262 / 0.14 ( 1) link_ALPHA1-3 : angle 1.79496 / 0.99 ( 3) link_ALPHA1-6 : bond 0.00681 / 0.36 ( 1) link_ALPHA1-6 : angle 1.72137 / 0.91 ( 3) link_BETA1-4 : bond 0.00092 / 0.05 ( 4) link_BETA1-4 : angle 1.87064 / 1.06 ( 12) link_NAG-ASN : bond 0.00425 / 0.26 ( 15) link_NAG-ASN : angle 2.11300 / 1.58 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.378 Fit side-chains REVERT: A 106 GLN cc_start: 0.7747 (mp-120) cc_final: 0.7510 (mp-120) REVERT: A 109 LEU cc_start: 0.7871 (tm) cc_final: 0.7575 (tt) REVERT: A 126 CYS cc_start: 0.5697 (OUTLIER) cc_final: 0.5117 (m) REVERT: A 157 HIS cc_start: 0.6698 (t70) cc_final: 0.6479 (t70) REVERT: A 191 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7458 (tpp-160) REVERT: A 213 TYR cc_start: 0.7068 (m-10) cc_final: 0.6757 (m-80) REVERT: A 348 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.8030 (m) REVERT: A 518 SER cc_start: 0.8346 (m) cc_final: 0.8136 (t) REVERT: A 651 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8319 (ttmt) REVERT: A 682 GLN cc_start: 0.8018 (mp10) cc_final: 0.7632 (mp10) REVERT: A 1039 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8133 (mm-40) outliers start: 34 outliers final: 21 residues processed: 190 average time/residue: 0.4907 time to fit residues: 100.9776 Evaluate side-chains 200 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1174 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 45 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.121611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104340 restraints weight = 12332.693| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.85 r_work: 0.3208 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9351 Z= 0.216 Angle : 0.635 11.318 12757 Z= 0.325 Chirality : 0.048 0.334 1515 Planarity : 0.004 0.041 1602 Dihedral : 6.325 57.856 1685 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.65 % Allowed : 12.07 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.24), residues: 1129 helix: 1.09 (0.36), residues: 212 sheet: -0.48 (0.29), residues: 300 loop : -1.05 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1085 TYR 0.019 0.002 TYR A 213 PHE 0.020 0.002 PHE A 91 TRP 0.008 0.002 TRP A 439 HIS 0.007 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 ( 9314) covalent geometry : angle 0.60481 / 0.31 (12662) SS BOND : bond 0.00531 / 0.29 ( 16) SS BOND : angle 2.89709 / 1.94 ( 32) hydrogen bonds : bond 0.03873 / 2.48 ( 319) hydrogen bonds : angle 5.46032 / 3.99 ( 969) link_ALPHA1-3 : bond 0.00443 / 0.23 ( 1) link_ALPHA1-3 : angle 1.72896 / 0.95 ( 3) link_ALPHA1-6 : bond 0.00597 / 0.31 ( 1) link_ALPHA1-6 : angle 1.57711 / 0.84 ( 3) link_BETA1-4 : bond 0.00041 / 0.02 ( 4) link_BETA1-4 : angle 1.80408 / 1.04 ( 12) link_NAG-ASN : bond 0.00391 / 0.24 ( 15) link_NAG-ASN : angle 2.03412 / 1.52 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.336 Fit side-chains REVERT: A 49 LEU cc_start: 0.8494 (mp) cc_final: 0.8263 (mt) REVERT: A 106 GLN cc_start: 0.7748 (mp-120) cc_final: 0.7512 (mp-120) REVERT: A 109 LEU cc_start: 0.7877 (tm) cc_final: 0.7591 (tt) REVERT: A 126 CYS cc_start: 0.5697 (OUTLIER) cc_final: 0.5101 (m) REVERT: A 157 HIS cc_start: 0.6699 (t70) cc_final: 0.6484 (t70) REVERT: A 191 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7401 (tpp-160) REVERT: A 213 TYR cc_start: 0.7182 (m-10) cc_final: 0.6835 (m-80) REVERT: A 347 PHE cc_start: 0.8074 (t80) cc_final: 0.7759 (t80) REVERT: A 348 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7927 (m) REVERT: A 518 SER cc_start: 0.8353 (m) cc_final: 0.8130 (t) REVERT: A 651 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8303 (ttmt) REVERT: A 682 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7627 (mp10) REVERT: A 1039 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8131 (mm-40) outliers start: 36 outliers final: 24 residues processed: 192 average time/residue: 0.5054 time to fit residues: 104.6109 Evaluate side-chains 202 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 470 GLN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1174 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 82 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 44 optimal weight: 0.7980 chunk 102 optimal weight: 0.3980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.105162 restraints weight = 12466.008| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.89 r_work: 0.3223 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9351 Z= 0.167 Angle : 0.615 11.521 12757 Z= 0.315 Chirality : 0.047 0.323 1515 Planarity : 0.004 0.084 1602 Dihedral : 6.208 57.263 1685 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.14 % Allowed : 12.68 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1129 helix: 1.23 (0.36), residues: 212 sheet: -0.42 (0.29), residues: 303 loop : -1.01 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 25 TYR 0.016 0.001 TYR A 213 PHE 0.016 0.002 PHE A 91 TRP 0.006 0.001 TRP A 439 HIS 0.005 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 9314) covalent geometry : angle 0.58733 / 0.31 (12662) SS BOND : bond 0.00572 / 0.30 ( 16) SS BOND : angle 2.72795 / 1.76 ( 32) hydrogen bonds : bond 0.03673 / 2.34 ( 319) hydrogen bonds : angle 5.38261 / 3.94 ( 969) link_ALPHA1-3 : bond 0.00467 / 0.25 ( 1) link_ALPHA1-3 : angle 1.55397 / 0.85 ( 3) link_ALPHA1-6 : bond 0.00632 / 0.33 ( 1) link_ALPHA1-6 : angle 1.48788 / 0.79 ( 3) link_BETA1-4 : bond 0.00082 / 0.04 ( 4) link_BETA1-4 : angle 1.71048 / 0.99 ( 12) link_NAG-ASN : bond 0.00347 / 0.23 ( 15) link_NAG-ASN : angle 1.90702 / 1.43 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.328 Fit side-chains REVERT: A 49 LEU cc_start: 0.8501 (mp) cc_final: 0.8280 (mt) REVERT: A 55 ILE cc_start: 0.5669 (OUTLIER) cc_final: 0.5426 (mp) REVERT: A 106 GLN cc_start: 0.7756 (mp-120) cc_final: 0.7516 (mp-120) REVERT: A 109 LEU cc_start: 0.7856 (tm) cc_final: 0.7579 (tt) REVERT: A 126 CYS cc_start: 0.5732 (OUTLIER) cc_final: 0.5128 (m) REVERT: A 191 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7285 (tpp-160) REVERT: A 213 TYR cc_start: 0.7215 (m-10) cc_final: 0.6820 (m-80) REVERT: A 347 PHE cc_start: 0.8024 (t80) cc_final: 0.7720 (t80) REVERT: A 348 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7854 (m) REVERT: A 518 SER cc_start: 0.8361 (m) cc_final: 0.8143 (t) REVERT: A 651 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8313 (ttmt) REVERT: A 682 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7645 (mp10) REVERT: A 1039 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8132 (mm-40) outliers start: 31 outliers final: 20 residues processed: 192 average time/residue: 0.4886 time to fit residues: 101.2693 Evaluate side-chains 202 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 470 GLN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1174 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 85 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 113 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 94 optimal weight: 0.7980 chunk 112 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 HIS ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.122704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.105399 restraints weight = 12385.257| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.86 r_work: 0.3224 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9351 Z= 0.168 Angle : 0.616 11.646 12757 Z= 0.317 Chirality : 0.047 0.323 1515 Planarity : 0.004 0.048 1602 Dihedral : 6.178 57.150 1685 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.74 % Allowed : 13.18 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1129 helix: 1.27 (0.36), residues: 211 sheet: -0.43 (0.29), residues: 302 loop : -1.01 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 25 TYR 0.016 0.001 TYR A 213 PHE 0.016 0.002 PHE A 91 TRP 0.006 0.001 TRP A 439 HIS 0.005 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 9314) covalent geometry : angle 0.58891 / 0.31 (12662) SS BOND : bond 0.00588 / 0.31 ( 16) SS BOND : angle 2.74057 / 1.76 ( 32) hydrogen bonds : bond 0.03656 / 2.33 ( 319) hydrogen bonds : angle 5.36183 / 3.93 ( 969) link_ALPHA1-3 : bond 0.00507 / 0.27 ( 1) link_ALPHA1-3 : angle 1.60740 / 0.88 ( 3) link_ALPHA1-6 : bond 0.00508 / 0.27 ( 1) link_ALPHA1-6 : angle 1.49205 / 0.79 ( 3) link_BETA1-4 : bond 0.00095 / 0.05 ( 4) link_BETA1-4 : angle 1.71091 / 0.99 ( 12) link_NAG-ASN : bond 0.00333 / 0.22 ( 15) link_NAG-ASN : angle 1.87851 / 1.41 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.346 Fit side-chains REVERT: A 49 LEU cc_start: 0.8523 (mp) cc_final: 0.8299 (mt) REVERT: A 55 ILE cc_start: 0.5594 (OUTLIER) cc_final: 0.5307 (mp) REVERT: A 106 GLN cc_start: 0.7774 (mp-120) cc_final: 0.7531 (mp-120) REVERT: A 109 LEU cc_start: 0.7844 (tm) cc_final: 0.7573 (tt) REVERT: A 126 CYS cc_start: 0.5716 (OUTLIER) cc_final: 0.5114 (m) REVERT: A 191 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7283 (tpp-160) REVERT: A 213 TYR cc_start: 0.7201 (m-10) cc_final: 0.6962 (m-80) REVERT: A 347 PHE cc_start: 0.7978 (t80) cc_final: 0.7666 (t80) REVERT: A 348 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7833 (p) REVERT: A 518 SER cc_start: 0.8392 (m) cc_final: 0.8178 (t) REVERT: A 542 PHE cc_start: 0.8335 (t80) cc_final: 0.8026 (t80) REVERT: A 651 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8309 (ttmt) REVERT: A 682 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7641 (mp10) REVERT: A 1039 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8138 (mm-40) outliers start: 27 outliers final: 20 residues processed: 192 average time/residue: 0.4606 time to fit residues: 95.5628 Evaluate side-chains 202 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 470 GLN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 860 GLN Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 929 LEU Chi-restraints excluded: chain A residue 1049 LEU Chi-restraints excluded: chain A residue 1174 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 0.5980 chunk 98 optimal weight: 0.0770 chunk 36 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 99 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 HIS ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 571 ASN A 577 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.105211 restraints weight = 12314.807| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.85 r_work: 0.3221 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9351 Z= 0.199 Angle : 0.640 14.669 12757 Z= 0.330 Chirality : 0.048 0.334 1515 Planarity : 0.005 0.096 1602 Dihedral : 6.253 57.540 1685 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.45 % Allowed : 12.68 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.24), residues: 1129 helix: 1.23 (0.36), residues: 211 sheet: -0.44 (0.29), residues: 303 loop : -1.05 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 25 TYR 0.018 0.002 TYR A 213 PHE 0.016 0.002 PHE A 91 TRP 0.008 0.001 TRP A 439 HIS 0.006 0.001 HIS A 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 9314) covalent geometry : angle 0.61231 / 0.32 (12662) SS BOND : bond 0.00648 / 0.34 ( 16) SS BOND : angle 2.83923 / 2.03 ( 32) hydrogen bonds : bond 0.03771 / 2.41 ( 319) hydrogen bonds : angle 5.38353 / 3.94 ( 969) link_ALPHA1-3 : bond 0.00440 / 0.23 ( 1) link_ALPHA1-3 : angle 1.72446 / 0.95 ( 3) link_ALPHA1-6 : bond 0.00437 / 0.23 ( 1) link_ALPHA1-6 : angle 1.57700 / 0.83 ( 3) link_BETA1-4 : bond 0.00055 / 0.03 ( 4) link_BETA1-4 : angle 1.78333 / 1.03 ( 12) link_NAG-ASN : bond 0.00374 / 0.24 ( 15) link_NAG-ASN : angle 1.95039 / 1.45 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3890.18 seconds wall clock time: 67 minutes 5.65 seconds (4025.65 seconds total)