Starting phenix.real_space_refine on Sat Sep 12 14:10:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w5v_21549/09_2026/6w5v_21549.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5v_21549/09_2026/6w5v_21549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6w5v_21549/09_2026/6w5v_21549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5v_21549/09_2026/6w5v_21549.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6w5v_21549/09_2026/6w5v_21549.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w5v_21549/09_2026/6w5v_21549.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w5v_21549/09_2026/6w5v_21549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5v_21549/09_2026/6w5v_21549.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6688 atoms to isotropic. 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 78 5.16 5 C 6855 2.51 5 N 1665 2.21 5 O 1988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s 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: 10586 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 9189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9189 Classifications: {'peptide': 1175} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1111} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1022 Classifications: {'peptide': 132} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 118} Chain: "B" 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 chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" 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 chiralities: 2 Chain: "F" 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 chiralities: 2 Chain: "G" 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 chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 182 Unusual residues: {'CLR': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'CLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.94, per 1000 atoms: 0.18 Number of scatterers: 10586 At special positions: 0 Unit cell: (135.908, 95.804, 153.732, 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 78 16.00 O 1988 8.00 N 1665 7.00 C 6855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.04 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.05 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.06 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.04 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=2.04 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.01 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.06 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.04 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.02 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.02 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 979 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 976 " distance=2.04 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 140 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 47 " distance=2.04 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 99 " distance=2.02 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 BETA1-3 " NAG C 2 " - " BMA C 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1401 " - " ASN A 452 " " NAG A1402 " - " ASN A 459 " " NAG A1405 " - " ASN A 524 " " NAG A1409 " - " ASN A 598 " " NAG A1410 " - " ASN A 916 " " NAG A1413 " - " ASN A 961 " " NAG A1414 " - " ASN A 968 " " NAG A1415 " - " ASN A1064 " " NAG A1418 " - " ASN A 158 " " NAG B 1 " - " ASN A 478 " " NAG C 1 " - " ASN A 557 " " NAG E 1 " - " ASN A 931 " " NAG F 1 " - " ASN A 222 " " NAG G 1 " - " ASN D 58 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 481.7 milliseconds 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2450 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 53.9% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.896A pdb=" N ASN A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 185 through 195 removed outlier: 4.246A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 268 through 295 removed outlier: 4.170A pdb=" N ALA A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 348 removed outlier: 4.159A pdb=" N GLU A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N CYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 376 through 382 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 436 through 453 removed outlier: 3.536A pdb=" N ASN A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 483 through 489 Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.759A pdb=" N ARG A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.570A pdb=" N VAL A 546 " --> pdb=" O PHE A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 542 through 546' Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 574 through 594 Processing helix chain 'A' and resid 607 through 618 removed outlier: 3.530A pdb=" N ASP A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 639 Processing helix chain 'A' and resid 653 through 679 Processing helix chain 'A' and resid 685 through 711 Proline residue: A 691 - end of helix Processing helix chain 'A' and resid 720 through 750 Proline residue: A 733 - end of helix Processing helix chain 'A' and resid 754 through 791 removed outlier: 4.104A pdb=" N SER A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU A 791 " --> pdb=" O ILE A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 833 through 852 removed outlier: 3.743A pdb=" N ILE A 837 " --> pdb=" O TRP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 856 Processing helix chain 'A' and resid 870 through 883 removed outlier: 3.976A pdb=" N ASP A 874 " --> pdb=" O SER A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 918 through 930 Processing helix chain 'A' and resid 941 through 951 removed outlier: 3.829A pdb=" N ASP A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1005 removed outlier: 4.484A pdb=" N MET A 996 " --> pdb=" O GLY A 992 " (cutoff:3.500A) Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1047 through 1069 Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1093 through 1117 Processing helix chain 'A' and resid 1120 through 1146 Processing helix chain 'A' and resid 1150 through 1177 removed outlier: 3.889A pdb=" N GLY A1162 " --> pdb=" O VAL A1158 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL A1165 " --> pdb=" O CYS A1161 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE A1167 " --> pdb=" O ILE A1163 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A1172 " --> pdb=" O CYS A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1202 removed outlier: 4.153A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A1200 " --> pdb=" O SER A1196 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A1202 " --> pdb=" O VAL A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1214 Processing helix chain 'A' and resid 1219 through 1242 removed outlier: 4.645A pdb=" N PHE A1226 " --> pdb=" O GLN A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1252 Processing helix chain 'D' and resid 91 through 96 removed outlier: 3.747A pdb=" N LYS D 94 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY D 96 " --> pdb=" O CYS D 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 129 removed outlier: 6.145A pdb=" N GLU A 143 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR A 126 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL A 141 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ASP A 128 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N THR A 139 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR A 206 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 144 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL A 208 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR A 146 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 404 through 405 Processing sheet with id=AA3, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA5, first strand: chain 'A' and resid 456 through 457 Processing sheet with id=AA6, first strand: chain 'A' and resid 1036 through 1043 removed outlier: 3.661A pdb=" N THR A1036 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A1038 " --> pdb=" O PHE A 891 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 958 through 959 Processing sheet with id=AA8, first strand: chain 'D' and resid 25 through 26 removed outlier: 6.185A pdb=" N LEU D 49 " --> pdb=" O VAL D 148 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 25 through 26 removed outlier: 6.565A pdb=" N LEU D 130 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS D 140 " --> pdb=" O TRP D 128 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP D 128 " --> pdb=" O CYS D 140 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU D 142 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL D 126 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU D 124 " --> pdb=" O PRO D 144 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 125 " --> pdb=" O ILE D 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 32 through 40 removed outlier: 6.593A pdb=" N THR D 60 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL D 37 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN D 58 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL D 39 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER D 56 " --> pdb=" O VAL D 39 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1506 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: 1.91 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3278 1.35 - 1.48: 2881 1.48 - 1.61: 4596 1.61 - 1.74: 0 1.74 - 1.87: 108 Bond restraints: 10863 Sorted by residual: bond pdb=" CA LEU A 748 " pdb=" C LEU A 748 " ideal model delta sigma weight residual 1.522 1.448 0.075 1.36e-02 5.41e+03 3.02e+01 bond pdb=" CA THR A 777 " pdb=" C THR A 777 " ideal model delta sigma weight residual 1.524 1.574 -0.051 1.26e-02 6.30e+03 1.61e+01 bond pdb=" CA ALA A1017 " pdb=" C ALA A1017 " ideal model delta sigma weight residual 1.522 1.474 0.049 1.37e-02 5.33e+03 1.26e+01 bond pdb=" C PHE A 565 " pdb=" N PRO A 566 " ideal model delta sigma weight residual 1.334 1.297 0.037 1.11e-02 8.12e+03 1.09e+01 bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 10858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 14632 4.69 - 9.38: 158 9.38 - 14.08: 21 14.08 - 18.77: 2 18.77 - 23.46: 1 Bond angle restraints: 14814 Sorted by residual: angle pdb=" N ASP A 551 " pdb=" CA ASP A 551 " pdb=" C ASP A 551 " ideal model delta sigma weight residual 112.72 126.58 -13.86 1.14e+00 7.69e-01 1.48e+02 angle pdb=" N THR A 777 " pdb=" CA THR A 777 " pdb=" C THR A 777 " ideal model delta sigma weight residual 111.14 123.53 -12.39 1.08e+00 8.57e-01 1.32e+02 angle pdb=" N ARG A 789 " pdb=" CA ARG A 789 " pdb=" C ARG A 789 " ideal model delta sigma weight residual 111.28 123.10 -11.82 1.09e+00 8.42e-01 1.18e+02 angle pdb=" C ARG A 372 " pdb=" CA ARG A 372 " pdb=" CB ARG A 372 " ideal model delta sigma weight residual 111.78 135.24 -23.46 2.20e+00 2.07e-01 1.14e+02 angle pdb=" N ILE A1202 " pdb=" CA ILE A1202 " pdb=" C ILE A1202 " ideal model delta sigma weight residual 110.72 121.40 -10.68 1.01e+00 9.80e-01 1.12e+02 ... (remaining 14809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5477 17.97 - 35.93: 532 35.93 - 53.90: 178 53.90 - 71.86: 52 71.86 - 89.83: 17 Dihedral angle restraints: 6256 sinusoidal: 2449 harmonic: 3807 Sorted by residual: dihedral pdb=" C ARG A 372 " pdb=" N ARG A 372 " pdb=" CA ARG A 372 " pdb=" CB ARG A 372 " ideal model delta harmonic sigma weight residual -122.60 -147.37 24.77 0 2.50e+00 1.60e-01 9.82e+01 dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 160 " pdb=" CB CYS A 160 " ideal model delta sinusoidal sigma weight residual 93.00 4.05 88.95 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS D 42 " pdb=" SG CYS D 42 " pdb=" SG CYS D 47 " pdb=" CB CYS D 47 " ideal model delta sinusoidal sigma weight residual 93.00 6.57 86.43 1 1.00e+01 1.00e-02 9.00e+01 ... (remaining 6253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.912: 1732 0.912 - 1.824: 1 1.824 - 2.736: 1 2.736 - 3.648: 0 3.648 - 4.560: 2 Chirality restraints: 1736 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 2.16 -4.56 2.00e-02 2.50e+03 5.20e+04 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 1.94 -4.34 2.00e-02 2.50e+03 4.72e+04 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-02 2.50e+03 1.59e+03 ... (remaining 1733 not shown) Planarity restraints: 1865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.340 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG F 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.502 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.283 2.00e-02 2.50e+03 2.43e-01 7.36e+02 pdb=" C7 NAG E 2 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.016 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.411 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 58 " 0.226 2.00e-02 2.50e+03 2.31e-01 6.68e+02 pdb=" CG ASN D 58 " -0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN D 58 " -0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN D 58 " -0.368 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.269 2.00e-02 2.50e+03 ... (remaining 1862 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 118 2.56 - 3.15: 9925 3.15 - 3.73: 16431 3.73 - 4.32: 22610 4.32 - 4.90: 36246 Nonbonded interactions: 85330 Sorted by model distance: nonbonded pdb=" OG SER A 741 " pdb=" CD1 ILE A1109 " model vdw 1.979 3.460 nonbonded pdb=" O3 NAG B 2 " pdb=" O7 NAG B 2 " model vdw 2.053 3.040 nonbonded pdb=" N TYR A 129 " pdb=" O LYS A 138 " model vdw 2.056 3.120 nonbonded pdb=" O ASP A 501 " pdb=" O PHE A 504 " model vdw 2.074 3.040 nonbonded pdb=" OG SER A 849 " pdb=" O VAL A1136 " model vdw 2.101 3.040 ... (remaining 85325 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 'B' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.500 Find NCS groups from input model: 0.070 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 : 0.009 0.277 10901 Z= 0.450 Angle : 1.694 53.823 14910 Z= 0.907 Chirality : 0.184 4.560 1736 Planarity : 0.012 0.287 1851 Dihedral : 16.885 89.830 3752 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 62.54 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.02 % Favored : 92.29 % Rotamer: Outliers : 9.99 % Allowed : 11.66 % Favored : 78.35 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.21 (0.22), residues: 1297 helix: -0.45 (0.21), residues: 594 sheet: -1.27 (0.43), residues: 133 loop : -2.65 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 607 TYR 0.025 0.002 TYR A 35 PHE 0.036 0.003 PHE A 503 TRP 0.056 0.004 TRP D 128 HIS 0.008 0.002 HIS A 497 Details of bonding type rmsd/Z covalent geometry : bond 0.00786 / 0.42 (10863) covalent geometry : angle 1.37242 / 0.84 (14814) SS BOND : bond 0.01428 / 0.91 ( 18) SS BOND : angle 3.84487 / 2.48 ( 36) hydrogen bonds : bond 0.17325 / 10.47 ( 529) hydrogen bonds : angle 7.50469 / 5.13 ( 1506) link_BETA1-3 : bond 0.06319 / 3.33 ( 1) link_BETA1-3 : angle 35.13511 / 18.47 ( 3) link_BETA1-4 : bond 0.04947 / 3.07 ( 5) link_BETA1-4 : angle 11.84022 / 7.08 ( 15) link_NAG-ASN : bond 0.08668 / 5.69 ( 14) link_NAG-ASN : angle 14.25422 / 8.89 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 335 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7664 (tpt-90) cc_final: 0.7410 (mmm160) REVERT: A 110 GLU cc_start: 0.7651 (pt0) cc_final: 0.7172 (pt0) REVERT: A 218 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8448 (tp30) REVERT: A 232 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7294 (t70) REVERT: A 233 GLU cc_start: 0.7730 (pt0) cc_final: 0.7238 (mp0) REVERT: A 235 THR cc_start: 0.8580 (m) cc_final: 0.8257 (p) REVERT: A 617 SER cc_start: 0.8283 (OUTLIER) cc_final: 0.7875 (t) REVERT: A 738 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8693 (p) REVERT: A 747 PHE cc_start: 0.8733 (m-10) cc_final: 0.7108 (t80) REVERT: A 754 MET cc_start: 0.7482 (tmm) cc_final: 0.7247 (tmm) REVERT: A 866 MET cc_start: 0.8210 (mmt) cc_final: 0.7541 (ptt) REVERT: A 899 TYR cc_start: 0.7566 (m-80) cc_final: 0.7278 (m-80) REVERT: A 928 GLN cc_start: 0.7856 (tp40) cc_final: 0.7609 (tp-100) REVERT: A 1025 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8454 (mp) REVERT: A 1101 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8198 (t0) REVERT: A 1133 MET cc_start: 0.8014 (ttt) cc_final: 0.7617 (ttt) REVERT: A 1137 ASN cc_start: 0.9000 (m-40) cc_final: 0.8776 (m110) REVERT: A 1138 MET cc_start: 0.8978 (tpt) cc_final: 0.8770 (tpp) REVERT: A 1173 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8171 (tpp80) REVERT: A 1194 MET cc_start: 0.8638 (tpp) cc_final: 0.8412 (mmt) REVERT: A 1218 SER cc_start: 0.7918 (OUTLIER) cc_final: 0.7603 (t) REVERT: A 1251 ILE cc_start: 0.8565 (mm) cc_final: 0.8340 (tt) REVERT: D 36 GLU cc_start: 0.6167 (tt0) cc_final: 0.5267 (tm-30) REVERT: D 56 SER cc_start: 0.9103 (OUTLIER) cc_final: 0.8851 (p) REVERT: D 64 ASN cc_start: 0.9133 (t0) cc_final: 0.8808 (m-40) REVERT: D 116 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7443 (ttpt) REVERT: D 129 GLN cc_start: 0.8006 (mt0) cc_final: 0.6890 (mt0) REVERT: D 131 GLN cc_start: 0.4671 (OUTLIER) cc_final: 0.4067 (mt0) REVERT: D 146 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7488 (pm20) outliers start: 114 outliers final: 28 residues processed: 398 average time/residue: 0.0894 time to fit residues: 51.0814 Evaluate side-chains 248 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 978 ARG Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1101 ASN Chi-restraints excluded: chain A residue 1173 ARG Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 131 GLN Chi-restraints excluded: chain D residue 146 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.7980 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 GLN A 41 ASN A 86 ASN A 92 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** A 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN A 614 ASN A 641 HIS ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 HIS A 988 GLN A1046 GLN A1170 HIS D 53 GLN D 66 GLN D 150 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.101038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.078974 restraints weight = 32338.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.081304 restraints weight = 17082.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.082767 restraints weight = 11268.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.083704 restraints weight = 8635.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.084254 restraints weight = 7284.927| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10901 Z= 0.196 Angle : 0.995 12.738 14910 Z= 0.467 Chirality : 0.055 0.535 1736 Planarity : 0.006 0.049 1851 Dihedral : 10.092 88.306 1502 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 5.61 % Allowed : 19.19 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.29 (0.22), residues: 1297 helix: 0.24 (0.20), residues: 607 sheet: -1.19 (0.42), residues: 139 loop : -2.00 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1183 TYR 0.021 0.002 TYR A1225 PHE 0.020 0.002 PHE A1243 TRP 0.027 0.003 TRP D 141 HIS 0.008 0.002 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (10863) covalent geometry : angle 0.93430 / 0.45 (14814) SS BOND : bond 0.00453 / 0.28 ( 18) SS BOND : angle 2.79240 / 1.56 ( 36) hydrogen bonds : bond 0.05355 / 3.32 ( 529) hydrogen bonds : angle 5.54723 / 3.84 ( 1506) link_BETA1-3 : bond 0.02759 / 1.45 ( 1) link_BETA1-3 : angle 8.08715 / 4.30 ( 3) link_BETA1-4 : bond 0.01471 / 0.73 ( 5) link_BETA1-4 : angle 4.55117 / 2.72 ( 15) link_NAG-ASN : bond 0.00863 / 0.48 ( 14) link_NAG-ASN : angle 4.98017 / 3.10 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 265 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7756 (tpt-90) cc_final: 0.7416 (mmm160) REVERT: A 147 TYR cc_start: 0.6709 (m-80) cc_final: 0.6036 (m-80) REVERT: A 217 MET cc_start: 0.5749 (mtm) cc_final: 0.4416 (mtm) REVERT: A 232 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7169 (t70) REVERT: A 233 GLU cc_start: 0.7756 (pt0) cc_final: 0.6955 (mp0) REVERT: A 235 THR cc_start: 0.8583 (m) cc_final: 0.8331 (p) REVERT: A 268 MET cc_start: 0.8846 (tpp) cc_final: 0.8607 (tpp) REVERT: A 754 MET cc_start: 0.8209 (tmm) cc_final: 0.7534 (tmm) REVERT: A 774 LEU cc_start: 0.8675 (mm) cc_final: 0.8474 (tp) REVERT: A 789 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.6072 (ptp-170) REVERT: A 899 TYR cc_start: 0.7504 (m-80) cc_final: 0.7057 (m-80) REVERT: A 912 MET cc_start: 0.7294 (mmm) cc_final: 0.6539 (ttm) REVERT: A 1133 MET cc_start: 0.7567 (ttt) cc_final: 0.7355 (ttt) REVERT: A 1161 CYS cc_start: 0.8418 (p) cc_final: 0.8019 (p) REVERT: A 1173 ARG cc_start: 0.8699 (tpp80) cc_final: 0.8326 (tpp80) REVERT: A 1251 ILE cc_start: 0.8700 (mm) cc_final: 0.8289 (tt) REVERT: D 36 GLU cc_start: 0.6835 (tt0) cc_final: 0.6081 (tp30) REVERT: D 64 ASN cc_start: 0.9180 (t0) cc_final: 0.8795 (m110) REVERT: D 75 HIS cc_start: 0.7996 (m-70) cc_final: 0.7284 (m-70) REVERT: D 146 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7332 (tm-30) outliers start: 64 outliers final: 28 residues processed: 305 average time/residue: 0.0779 time to fit residues: 36.1682 Evaluate side-chains 243 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 978 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1254 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 146 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 54 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN D 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.097889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075671 restraints weight = 33597.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.077928 restraints weight = 17621.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.079398 restraints weight = 11626.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.080355 restraints weight = 8885.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.080908 restraints weight = 7471.833| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10901 Z= 0.216 Angle : 0.903 12.375 14910 Z= 0.427 Chirality : 0.052 0.376 1736 Planarity : 0.005 0.045 1851 Dihedral : 8.125 74.779 1450 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 5.43 % Allowed : 23.75 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.93 (0.23), residues: 1297 helix: 0.44 (0.20), residues: 621 sheet: -1.01 (0.40), residues: 150 loop : -1.75 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1183 TYR 0.026 0.002 TYR A1225 PHE 0.019 0.002 PHE A 503 TRP 0.022 0.002 TRP D 141 HIS 0.005 0.001 HIS A 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (10863) covalent geometry : angle 0.85504 / 0.41 (14814) SS BOND : bond 0.00668 / 0.35 ( 18) SS BOND : angle 2.74069 / 1.45 ( 36) hydrogen bonds : bond 0.04999 / 3.07 ( 529) hydrogen bonds : angle 5.42311 / 3.82 ( 1506) link_BETA1-3 : bond 0.01986 / 1.05 ( 1) link_BETA1-3 : angle 6.94956 / 3.70 ( 3) link_BETA1-4 : bond 0.01121 / 0.57 ( 5) link_BETA1-4 : angle 3.53059 / 2.04 ( 15) link_NAG-ASN : bond 0.00699 / 0.40 ( 14) link_NAG-ASN : angle 4.12741 / 2.49 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 216 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7891 (tpt-90) cc_final: 0.7602 (mmm-85) REVERT: A 147 TYR cc_start: 0.7071 (m-80) cc_final: 0.6373 (m-80) REVERT: A 217 MET cc_start: 0.5993 (mtm) cc_final: 0.4609 (mtm) REVERT: A 233 GLU cc_start: 0.7859 (pt0) cc_final: 0.7076 (mp0) REVERT: A 235 THR cc_start: 0.8530 (m) cc_final: 0.8239 (p) REVERT: A 268 MET cc_start: 0.8960 (tpp) cc_final: 0.8751 (tpp) REVERT: A 487 TYR cc_start: 0.8489 (m-80) cc_final: 0.8249 (m-80) REVERT: A 754 MET cc_start: 0.8175 (tmm) cc_final: 0.7198 (tmm) REVERT: A 774 LEU cc_start: 0.8825 (mm) cc_final: 0.8560 (tp) REVERT: A 789 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.5985 (ptp-170) REVERT: A 899 TYR cc_start: 0.7564 (m-80) cc_final: 0.6927 (m-80) REVERT: A 1122 TRP cc_start: 0.6493 (OUTLIER) cc_final: 0.5931 (m100) REVERT: A 1173 ARG cc_start: 0.8678 (tpp80) cc_final: 0.8241 (tpp80) REVERT: A 1222 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8222 (pt0) REVERT: D 36 GLU cc_start: 0.7110 (tt0) cc_final: 0.6324 (tp30) REVERT: D 64 ASN cc_start: 0.9322 (t0) cc_final: 0.8848 (m110) REVERT: D 75 HIS cc_start: 0.8331 (m-70) cc_final: 0.8113 (m90) REVERT: D 85 PHE cc_start: 0.7458 (t80) cc_final: 0.7104 (t80) REVERT: D 104 ASP cc_start: 0.9317 (m-30) cc_final: 0.8662 (p0) REVERT: D 146 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7154 (tm-30) outliers start: 62 outliers final: 45 residues processed: 258 average time/residue: 0.0792 time to fit residues: 31.4284 Evaluate side-chains 241 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 552 ASP Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 978 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1122 TRP Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1222 GLN Chi-restraints excluded: chain A residue 1254 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 146 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 5 optimal weight: 0.0670 chunk 62 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 80 optimal weight: 0.0570 chunk 72 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.9838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.099506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.077218 restraints weight = 32850.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.079596 restraints weight = 16940.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.081089 restraints weight = 11065.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.082083 restraints weight = 8423.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.082696 restraints weight = 7063.343| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10901 Z= 0.149 Angle : 0.851 13.407 14910 Z= 0.394 Chirality : 0.049 0.361 1736 Planarity : 0.005 0.045 1851 Dihedral : 7.391 66.924 1444 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 5.08 % Allowed : 24.45 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 (0.23), residues: 1297 helix: 0.66 (0.20), residues: 613 sheet: -0.93 (0.40), residues: 148 loop : -1.60 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1183 TYR 0.026 0.001 TYR A1225 PHE 0.017 0.001 PHE A 632 TRP 0.018 0.002 TRP D 141 HIS 0.003 0.001 HIS A 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (10863) covalent geometry : angle 0.80827 / 0.38 (14814) SS BOND : bond 0.00535 / 0.30 ( 18) SS BOND : angle 2.67912 / 1.39 ( 36) hydrogen bonds : bond 0.04634 / 2.84 ( 529) hydrogen bonds : angle 5.18427 / 3.65 ( 1506) link_BETA1-3 : bond 0.01736 / 0.91 ( 1) link_BETA1-3 : angle 5.56458 / 2.98 ( 3) link_BETA1-4 : bond 0.01030 / 0.52 ( 5) link_BETA1-4 : angle 3.35699 / 1.94 ( 15) link_NAG-ASN : bond 0.00737 / 0.43 ( 14) link_NAG-ASN : angle 3.74896 / 2.23 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 223 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7882 (tpt-90) cc_final: 0.7532 (mmm-85) REVERT: A 233 GLU cc_start: 0.7808 (pt0) cc_final: 0.6839 (mp0) REVERT: A 754 MET cc_start: 0.8117 (tmm) cc_final: 0.7254 (tmm) REVERT: A 774 LEU cc_start: 0.8927 (mm) cc_final: 0.8491 (tp) REVERT: A 789 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5800 (ptt180) REVERT: A 899 TYR cc_start: 0.7429 (m-80) cc_final: 0.6673 (m-80) REVERT: A 1122 TRP cc_start: 0.6379 (m-10) cc_final: 0.5885 (m100) REVERT: A 1173 ARG cc_start: 0.8777 (tpp80) cc_final: 0.8350 (tpp80) REVERT: D 36 GLU cc_start: 0.7219 (tt0) cc_final: 0.6719 (tp30) REVERT: D 64 ASN cc_start: 0.9273 (t0) cc_final: 0.8848 (m110) REVERT: D 75 HIS cc_start: 0.8262 (m-70) cc_final: 0.7703 (m90) REVERT: D 104 ASP cc_start: 0.9201 (m-30) cc_final: 0.8555 (p0) REVERT: D 112 LYS cc_start: 0.8191 (tptt) cc_final: 0.7344 (mmtm) REVERT: D 146 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7405 (tm-30) outliers start: 58 outliers final: 34 residues processed: 262 average time/residue: 0.0746 time to fit residues: 30.3528 Evaluate side-chains 231 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1254 SER Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 146 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 100 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 0.0770 chunk 85 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 overall best weight: 2.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.098183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.075973 restraints weight = 33109.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.078268 restraints weight = 17429.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.079710 restraints weight = 11508.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.080690 restraints weight = 8833.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.081257 restraints weight = 7418.439| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 10901 Z= 0.187 Angle : 0.852 13.760 14910 Z= 0.400 Chirality : 0.049 0.350 1736 Planarity : 0.004 0.045 1851 Dihedral : 7.310 59.778 1439 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.43 % Allowed : 25.42 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -0.53 (0.23), residues: 1297 helix: 0.76 (0.21), residues: 623 sheet: -0.88 (0.40), residues: 151 loop : -1.53 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 978 TYR 0.024 0.002 TYR A1225 PHE 0.020 0.002 PHE A 769 TRP 0.015 0.002 TRP A 27 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (10863) covalent geometry : angle 0.81381 / 0.39 (14814) SS BOND : bond 0.00397 / 0.24 ( 18) SS BOND : angle 2.61960 / 1.28 ( 36) hydrogen bonds : bond 0.04586 / 2.80 ( 529) hydrogen bonds : angle 5.18755 / 3.65 ( 1506) link_BETA1-3 : bond 0.01660 / 0.87 ( 1) link_BETA1-3 : angle 5.00831 / 2.69 ( 3) link_BETA1-4 : bond 0.00883 / 0.45 ( 5) link_BETA1-4 : angle 3.15214 / 1.81 ( 15) link_NAG-ASN : bond 0.00652 / 0.36 ( 14) link_NAG-ASN : angle 3.61248 / 2.14 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 204 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7890 (tpt-90) cc_final: 0.7438 (mmm160) REVERT: A 233 GLU cc_start: 0.7850 (pt0) cc_final: 0.7041 (mp0) REVERT: A 754 MET cc_start: 0.8163 (tmm) cc_final: 0.7188 (tmm) REVERT: A 774 LEU cc_start: 0.9022 (mm) cc_final: 0.8507 (tp) REVERT: A 789 ARG cc_start: 0.5972 (OUTLIER) cc_final: 0.5607 (ptt180) REVERT: A 899 TYR cc_start: 0.7357 (m-80) cc_final: 0.6769 (m-80) REVERT: A 1122 TRP cc_start: 0.6492 (OUTLIER) cc_final: 0.5880 (m100) REVERT: A 1173 ARG cc_start: 0.8788 (tpp80) cc_final: 0.8333 (tpp80) REVERT: D 36 GLU cc_start: 0.7200 (tt0) cc_final: 0.6213 (tp30) REVERT: D 64 ASN cc_start: 0.9207 (t0) cc_final: 0.8820 (m110) REVERT: D 75 HIS cc_start: 0.8340 (m-70) cc_final: 0.8106 (m90) REVERT: D 104 ASP cc_start: 0.9219 (m-30) cc_final: 0.8589 (p0) REVERT: D 146 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7623 (tm-30) outliers start: 62 outliers final: 44 residues processed: 244 average time/residue: 0.0757 time to fit residues: 28.5456 Evaluate side-chains 236 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1122 TRP Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1254 SER Chi-restraints excluded: chain D residue 146 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 90 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 0.1980 chunk 111 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.099411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.077344 restraints weight = 33177.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.079717 restraints weight = 16967.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.081211 restraints weight = 11066.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.082202 restraints weight = 8411.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.082869 restraints weight = 7043.949| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10901 Z= 0.142 Angle : 0.834 12.423 14910 Z= 0.383 Chirality : 0.049 0.343 1736 Planarity : 0.004 0.043 1851 Dihedral : 7.086 59.290 1439 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.73 % Allowed : 27.08 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.42 (0.23), residues: 1297 helix: 0.82 (0.21), residues: 621 sheet: -0.65 (0.41), residues: 151 loop : -1.49 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1183 TYR 0.022 0.001 TYR D 109 PHE 0.018 0.001 PHE A 632 TRP 0.013 0.001 TRP D 141 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (10863) covalent geometry : angle 0.80367 / 0.38 (14814) SS BOND : bond 0.00284 / 0.18 ( 18) SS BOND : angle 1.75996 / 0.93 ( 36) hydrogen bonds : bond 0.04386 / 2.67 ( 529) hydrogen bonds : angle 5.09538 / 3.56 ( 1506) link_BETA1-3 : bond 0.01315 / 0.69 ( 1) link_BETA1-3 : angle 4.44065 / 2.39 ( 3) link_BETA1-4 : bond 0.00973 / 0.50 ( 5) link_BETA1-4 : angle 3.05247 / 1.74 ( 15) link_NAG-ASN : bond 0.00718 / 0.42 ( 14) link_NAG-ASN : angle 3.39882 / 2.00 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7979 (tpt-90) cc_final: 0.7538 (mmm160) REVERT: A 233 GLU cc_start: 0.7927 (pt0) cc_final: 0.7019 (mp0) REVERT: A 754 MET cc_start: 0.8068 (tmm) cc_final: 0.7105 (tmm) REVERT: A 774 LEU cc_start: 0.9022 (mm) cc_final: 0.8441 (tp) REVERT: A 789 ARG cc_start: 0.5690 (OUTLIER) cc_final: 0.5356 (ptt180) REVERT: A 1122 TRP cc_start: 0.6465 (m-10) cc_final: 0.5926 (m100) REVERT: A 1159 MET cc_start: 0.8834 (tmm) cc_final: 0.8462 (ttp) REVERT: A 1173 ARG cc_start: 0.8719 (tpp80) cc_final: 0.8175 (tpp80) REVERT: A 1179 MET cc_start: 0.6265 (mmt) cc_final: 0.6060 (mmt) REVERT: A 1223 ILE cc_start: 0.8570 (mt) cc_final: 0.8276 (mt) REVERT: D 36 GLU cc_start: 0.7368 (tt0) cc_final: 0.6327 (tp30) REVERT: D 64 ASN cc_start: 0.9266 (t0) cc_final: 0.8893 (m110) REVERT: D 75 HIS cc_start: 0.8202 (m-70) cc_final: 0.7747 (m90) REVERT: D 104 ASP cc_start: 0.9116 (m-30) cc_final: 0.8566 (p0) REVERT: D 112 LYS cc_start: 0.8119 (tptt) cc_final: 0.7469 (mmtm) outliers start: 54 outliers final: 41 residues processed: 255 average time/residue: 0.0743 time to fit residues: 29.5555 Evaluate side-chains 241 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 976 CYS Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1254 SER Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 111 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 5 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 HIS ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.099785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.078264 restraints weight = 32597.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.080559 restraints weight = 17282.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.082056 restraints weight = 11409.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.082973 restraints weight = 8675.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.083615 restraints weight = 7299.537| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10901 Z= 0.140 Angle : 0.815 12.877 14910 Z= 0.375 Chirality : 0.048 0.339 1736 Planarity : 0.004 0.043 1851 Dihedral : 6.712 58.971 1436 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.47 % Allowed : 28.05 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.23), residues: 1297 helix: 0.89 (0.21), residues: 620 sheet: -0.56 (0.42), residues: 145 loop : -1.46 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1183 TYR 0.016 0.001 TYR A1229 PHE 0.024 0.001 PHE A 769 TRP 0.020 0.001 TRP A 27 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (10863) covalent geometry : angle 0.78602 / 0.37 (14814) SS BOND : bond 0.00284 / 0.17 ( 18) SS BOND : angle 1.96653 / 1.01 ( 36) hydrogen bonds : bond 0.04322 / 2.62 ( 529) hydrogen bonds : angle 5.04408 / 3.51 ( 1506) link_BETA1-3 : bond 0.01187 / 0.62 ( 1) link_BETA1-3 : angle 4.14093 / 2.23 ( 3) link_BETA1-4 : bond 0.00903 / 0.47 ( 5) link_BETA1-4 : angle 2.94814 / 1.67 ( 15) link_NAG-ASN : bond 0.00686 / 0.39 ( 14) link_NAG-ASN : angle 3.21788 / 1.88 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 211 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7957 (tpt-90) cc_final: 0.7693 (mmm-85) REVERT: A 193 MET cc_start: 0.9173 (tpp) cc_final: 0.8802 (tpp) REVERT: A 233 GLU cc_start: 0.7892 (pt0) cc_final: 0.7012 (mp0) REVERT: A 754 MET cc_start: 0.8127 (tmm) cc_final: 0.7174 (tmm) REVERT: A 789 ARG cc_start: 0.5717 (OUTLIER) cc_final: 0.5324 (ptt180) REVERT: A 1122 TRP cc_start: 0.6248 (m-10) cc_final: 0.5926 (m100) REVERT: A 1159 MET cc_start: 0.8814 (tmm) cc_final: 0.8409 (ttp) REVERT: A 1160 SER cc_start: 0.9314 (m) cc_final: 0.8743 (m) REVERT: A 1173 ARG cc_start: 0.8624 (tpp80) cc_final: 0.8278 (tpp80) REVERT: A 1179 MET cc_start: 0.6252 (mmt) cc_final: 0.6049 (mmt) REVERT: A 1223 ILE cc_start: 0.8595 (mt) cc_final: 0.8334 (mt) REVERT: D 36 GLU cc_start: 0.7359 (tt0) cc_final: 0.6337 (tp30) REVERT: D 64 ASN cc_start: 0.9273 (t0) cc_final: 0.8946 (m110) REVERT: D 75 HIS cc_start: 0.8110 (m-70) cc_final: 0.7698 (m90) REVERT: D 111 ASN cc_start: 0.4879 (OUTLIER) cc_final: 0.4670 (t0) outliers start: 51 outliers final: 41 residues processed: 247 average time/residue: 0.0741 time to fit residues: 28.3303 Evaluate side-chains 243 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 976 CYS Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1154 LEU Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1254 SER Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 122 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 95 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 4 optimal weight: 0.0060 chunk 96 optimal weight: 4.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS A 554 ASN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.097485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.075837 restraints weight = 33135.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.078057 restraints weight = 17783.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.079454 restraints weight = 11845.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.080391 restraints weight = 9137.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.081002 restraints weight = 7690.220| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10901 Z= 0.205 Angle : 0.856 12.776 14910 Z= 0.400 Chirality : 0.049 0.325 1736 Planarity : 0.004 0.041 1851 Dihedral : 6.723 58.282 1436 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 5.26 % Allowed : 27.70 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -0.41 (0.23), residues: 1297 helix: 0.77 (0.21), residues: 622 sheet: -0.40 (0.44), residues: 147 loop : -1.48 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 411 TYR 0.023 0.002 TYR D 109 PHE 0.023 0.002 PHE A 632 TRP 0.017 0.002 TRP A 27 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (10863) covalent geometry : angle 0.82859 / 0.39 (14814) SS BOND : bond 0.00335 / 0.22 ( 18) SS BOND : angle 1.96914 / 1.03 ( 36) hydrogen bonds : bond 0.04544 / 2.75 ( 529) hydrogen bonds : angle 5.20976 / 3.63 ( 1506) link_BETA1-3 : bond 0.01190 / 0.63 ( 1) link_BETA1-3 : angle 4.19357 / 2.27 ( 3) link_BETA1-4 : bond 0.00816 / 0.43 ( 5) link_BETA1-4 : angle 2.94199 / 1.66 ( 15) link_NAG-ASN : bond 0.00587 / 0.31 ( 14) link_NAG-ASN : angle 3.21858 / 1.91 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 193 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8060 (tpt-90) cc_final: 0.7788 (mmm-85) REVERT: A 147 TYR cc_start: 0.7172 (m-80) cc_final: 0.6654 (m-80) REVERT: A 193 MET cc_start: 0.9211 (tpp) cc_final: 0.8987 (tpp) REVERT: A 233 GLU cc_start: 0.7919 (pt0) cc_final: 0.7058 (mp0) REVERT: A 594 TYR cc_start: 0.8107 (t80) cc_final: 0.7496 (t80) REVERT: A 754 MET cc_start: 0.8249 (tmm) cc_final: 0.7252 (tmm) REVERT: A 774 LEU cc_start: 0.9023 (mm) cc_final: 0.8460 (tp) REVERT: A 789 ARG cc_start: 0.5798 (OUTLIER) cc_final: 0.5360 (ptp-170) REVERT: A 1122 TRP cc_start: 0.6411 (m-10) cc_final: 0.6127 (m100) REVERT: A 1159 MET cc_start: 0.9046 (tmm) cc_final: 0.8742 (ppp) REVERT: A 1173 ARG cc_start: 0.8592 (tpp80) cc_final: 0.8267 (tpp80) REVERT: A 1179 MET cc_start: 0.6345 (mmt) cc_final: 0.6095 (mmt) REVERT: A 1223 ILE cc_start: 0.8626 (mt) cc_final: 0.8359 (mt) REVERT: D 36 GLU cc_start: 0.7468 (tt0) cc_final: 0.7265 (tt0) REVERT: D 64 ASN cc_start: 0.9225 (t0) cc_final: 0.8926 (m-40) REVERT: D 75 HIS cc_start: 0.8223 (m-70) cc_final: 0.7813 (m90) REVERT: D 111 ASN cc_start: 0.5013 (OUTLIER) cc_final: 0.4807 (t0) outliers start: 60 outliers final: 51 residues processed: 236 average time/residue: 0.0799 time to fit residues: 29.4757 Evaluate side-chains 240 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 187 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 976 CYS Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1254 SER Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 122 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 123 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.098988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.077368 restraints weight = 33135.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.079629 restraints weight = 17606.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.081089 restraints weight = 11663.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.082006 restraints weight = 8911.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.082619 restraints weight = 7486.925| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10901 Z= 0.149 Angle : 0.826 13.579 14910 Z= 0.384 Chirality : 0.048 0.300 1736 Planarity : 0.004 0.041 1851 Dihedral : 6.587 59.060 1436 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.29 % Allowed : 28.75 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.24), residues: 1297 helix: 0.80 (0.21), residues: 621 sheet: -0.31 (0.44), residues: 147 loop : -1.42 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 337 TYR 0.016 0.001 TYR A1229 PHE 0.022 0.001 PHE A 632 TRP 0.017 0.002 TRP A 27 HIS 0.005 0.001 HIS A1239 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (10863) covalent geometry : angle 0.80064 / 0.38 (14814) SS BOND : bond 0.00322 / 0.20 ( 18) SS BOND : angle 1.58584 / 0.89 ( 36) hydrogen bonds : bond 0.04405 / 2.66 ( 529) hydrogen bonds : angle 5.10029 / 3.55 ( 1506) link_BETA1-3 : bond 0.00983 / 0.52 ( 1) link_BETA1-3 : angle 4.08850 / 2.20 ( 3) link_BETA1-4 : bond 0.00832 / 0.45 ( 5) link_BETA1-4 : angle 2.87126 / 1.62 ( 15) link_NAG-ASN : bond 0.00656 / 0.37 ( 14) link_NAG-ASN : angle 3.12871 / 1.85 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 199 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8070 (tpt-90) cc_final: 0.7822 (mmm-85) REVERT: A 110 GLU cc_start: 0.8266 (pt0) cc_final: 0.7835 (pt0) REVERT: A 147 TYR cc_start: 0.7130 (m-80) cc_final: 0.6617 (m-80) REVERT: A 162 ASP cc_start: 0.7931 (m-30) cc_final: 0.7307 (m-30) REVERT: A 193 MET cc_start: 0.9211 (tpp) cc_final: 0.8975 (tpp) REVERT: A 754 MET cc_start: 0.8226 (tmm) cc_final: 0.7113 (tmm) REVERT: A 789 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5350 (ptt180) REVERT: A 1122 TRP cc_start: 0.6341 (m-10) cc_final: 0.6076 (m100) REVERT: A 1159 MET cc_start: 0.8912 (tmm) cc_final: 0.8700 (tmm) REVERT: A 1160 SER cc_start: 0.9499 (m) cc_final: 0.9208 (m) REVERT: A 1173 ARG cc_start: 0.8568 (tpp80) cc_final: 0.8218 (tpp80) REVERT: A 1179 MET cc_start: 0.6282 (mmt) cc_final: 0.5990 (mmt) REVERT: A 1194 MET cc_start: 0.8715 (mmm) cc_final: 0.7887 (tpt) REVERT: A 1223 ILE cc_start: 0.8577 (mt) cc_final: 0.8310 (mt) REVERT: D 64 ASN cc_start: 0.9217 (t0) cc_final: 0.8915 (m-40) REVERT: D 75 HIS cc_start: 0.8149 (m-70) cc_final: 0.7731 (m90) REVERT: D 111 ASN cc_start: 0.4371 (OUTLIER) cc_final: 0.4136 (t0) outliers start: 49 outliers final: 44 residues processed: 233 average time/residue: 0.0793 time to fit residues: 28.6835 Evaluate side-chains 240 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 976 CYS Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 122 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 119 optimal weight: 0.0570 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.098565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.076961 restraints weight = 32754.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.079317 restraints weight = 16924.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.080853 restraints weight = 11001.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.081808 restraints weight = 8261.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.082395 restraints weight = 6894.954| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10901 Z= 0.159 Angle : 0.832 13.555 14910 Z= 0.385 Chirality : 0.048 0.306 1736 Planarity : 0.004 0.041 1851 Dihedral : 6.539 59.016 1436 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.21 % Allowed : 29.54 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.24), residues: 1297 helix: 0.78 (0.21), residues: 621 sheet: -0.31 (0.45), residues: 145 loop : -1.40 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1183 TYR 0.016 0.001 TYR A1229 PHE 0.023 0.001 PHE A 632 TRP 0.019 0.002 TRP A1143 HIS 0.007 0.001 HIS A1239 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (10863) covalent geometry : angle 0.80689 / 0.38 (14814) SS BOND : bond 0.00300 / 0.20 ( 18) SS BOND : angle 1.64330 / 0.91 ( 36) hydrogen bonds : bond 0.04349 / 2.63 ( 529) hydrogen bonds : angle 5.12549 / 3.56 ( 1506) link_BETA1-3 : bond 0.00867 / 0.46 ( 1) link_BETA1-3 : angle 4.12509 / 2.22 ( 3) link_BETA1-4 : bond 0.00843 / 0.46 ( 5) link_BETA1-4 : angle 2.81176 / 1.58 ( 15) link_NAG-ASN : bond 0.00630 / 0.35 ( 14) link_NAG-ASN : angle 3.08129 / 1.82 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2594 Ramachandran restraints generated. 1297 Oldfield, 0 Emsley, 1297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8079 (tpt-90) cc_final: 0.7834 (mmm-85) REVERT: A 110 GLU cc_start: 0.8015 (pt0) cc_final: 0.7348 (pt0) REVERT: A 147 TYR cc_start: 0.7162 (m-80) cc_final: 0.6631 (m-80) REVERT: A 162 ASP cc_start: 0.7959 (m-30) cc_final: 0.7316 (m-30) REVERT: A 193 MET cc_start: 0.9212 (tpp) cc_final: 0.9002 (tpp) REVERT: A 754 MET cc_start: 0.8214 (tmm) cc_final: 0.7095 (tmm) REVERT: A 789 ARG cc_start: 0.5538 (OUTLIER) cc_final: 0.5088 (ptt180) REVERT: A 1122 TRP cc_start: 0.6377 (m-10) cc_final: 0.6137 (m100) REVERT: A 1160 SER cc_start: 0.9519 (m) cc_final: 0.9263 (m) REVERT: A 1173 ARG cc_start: 0.8560 (tpp80) cc_final: 0.8223 (tpp80) REVERT: A 1194 MET cc_start: 0.8711 (mmm) cc_final: 0.7940 (tpt) REVERT: A 1219 GLN cc_start: 0.8330 (mt0) cc_final: 0.7955 (mt0) REVERT: A 1223 ILE cc_start: 0.8562 (mt) cc_final: 0.8313 (mt) REVERT: D 64 ASN cc_start: 0.9175 (t0) cc_final: 0.8878 (m-40) REVERT: D 75 HIS cc_start: 0.8211 (m-70) cc_final: 0.7817 (m90) outliers start: 48 outliers final: 45 residues processed: 230 average time/residue: 0.0780 time to fit residues: 28.0292 Evaluate side-chains 238 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 700 ASP Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 789 ARG Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 976 CYS Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1040 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1117 LEU Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 122 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 48 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 128 optimal weight: 30.0000 chunk 43 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 HIS ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.100320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.078709 restraints weight = 32827.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.081128 restraints weight = 17086.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.082653 restraints weight = 11124.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.083633 restraints weight = 8400.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.084256 restraints weight = 6993.951| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10901 Z= 0.139 Angle : 0.837 13.464 14910 Z= 0.385 Chirality : 0.047 0.299 1736 Planarity : 0.004 0.041 1851 Dihedral : 6.436 59.857 1436 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.21 % Allowed : 29.80 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.26 (0.24), residues: 1297 helix: 0.84 (0.21), residues: 622 sheet: -0.15 (0.45), residues: 144 loop : -1.38 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 978 TYR 0.021 0.001 TYR A1229 PHE 0.019 0.001 PHE A 632 TRP 0.020 0.002 TRP A1143 HIS 0.008 0.001 HIS A1239 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (10863) covalent geometry : angle 0.81265 / 0.38 (14814) SS BOND : bond 0.00255 / 0.16 ( 18) SS BOND : angle 1.88945 / 1.00 ( 36) hydrogen bonds : bond 0.04180 / 2.52 ( 529) hydrogen bonds : angle 5.03327 / 3.49 ( 1506) link_BETA1-3 : bond 0.00713 / 0.38 ( 1) link_BETA1-3 : angle 4.01564 / 2.14 ( 3) link_BETA1-4 : bond 0.00861 / 0.47 ( 5) link_BETA1-4 : angle 2.74238 / 1.53 ( 15) link_NAG-ASN : bond 0.00673 / 0.38 ( 14) link_NAG-ASN : angle 2.97336 / 1.75 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1932.36 seconds wall clock time: 34 minutes 14.46 seconds (2054.46 seconds total)