Starting phenix.real_space_refine on Wed Mar 4 20:46:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w5v_21549/03_2026/6w5v_21549.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5v_21549/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6w5v_21549/03_2026/6w5v_21549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5v_21549/03_2026/6w5v_21549.map" model { file = "/net/cci-nas-00/data/ceres_data/6w5v_21549/03_2026/6w5v_21549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5v_21549/03_2026/6w5v_21549.cif" } 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-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 27 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.23, per 1000 atoms: 0.21 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: 1.03 Conformation dependent library (CDL) restraints added in 524.0 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: 0.38 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: 1.63 Time building geometry restraints manager: 1.35 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 - 26.61: 6304 26.61 - 53.23: 418 53.23 - 79.84: 96 79.84 - 106.46: 27 106.46 - 133.07: 18 Dihedral angle restraints: 6863 sinusoidal: 3056 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 6860 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.760 Find NCS groups from input model: 0.040 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 19.775 133.072 4359 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 covalent geometry : bond 0.00786 (10863) covalent geometry : angle 1.37242 (14814) SS BOND : bond 0.01428 ( 18) SS BOND : angle 3.84487 ( 36) hydrogen bonds : bond 0.17325 ( 529) hydrogen bonds : angle 7.50469 ( 1506) link_BETA1-3 : bond 0.06319 ( 1) link_BETA1-3 : angle 35.13511 ( 3) link_BETA1-4 : bond 0.04947 ( 5) link_BETA1-4 : angle 11.84022 ( 15) link_NAG-ASN : bond 0.08668 ( 14) link_NAG-ASN : angle 14.25422 ( 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 : 0.366 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: 0.0954 time to fit residues: 54.3490 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 : 0.309 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3702 r_free = 0.3702 target = 0.101071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.079036 restraints weight = 32306.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.081347 restraints weight = 17010.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.082821 restraints weight = 11218.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.083747 restraints weight = 8580.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.084271 restraints weight = 7251.384| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10901 Z= 0.196 Angle : 1.002 12.564 14910 Z= 0.468 Chirality : 0.054 0.469 1736 Planarity : 0.006 0.049 1851 Dihedral : 14.874 103.559 2109 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.96 % Allowed : 18.76 % Favored : 75.28 % 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: 0.21 (0.20), residues: 608 sheet: -1.17 (0.43), residues: 138 loop : -1.98 (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 0.021 0.002 PHE A1243 TRP 0.031 0.003 TRP D 141 HIS 0.008 0.002 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00424 (10863) covalent geometry : angle 0.94105 (14814) SS BOND : bond 0.00426 ( 18) SS BOND : angle 2.75310 ( 36) hydrogen bonds : bond 0.05311 ( 529) hydrogen bonds : angle 5.52919 ( 1506) link_BETA1-3 : bond 0.02782 ( 1) link_BETA1-3 : angle 7.86101 ( 3) link_BETA1-4 : bond 0.01471 ( 5) link_BETA1-4 : angle 4.63452 ( 15) link_NAG-ASN : bond 0.00843 ( 14) link_NAG-ASN : angle 5.06779 ( 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 338 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 270 time to evaluate : 0.287 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: 0.7758 (tpt-90) cc_final: 0.7421 (mmm160) REVERT: A 147 TYR cc_start: 0.6720 (m-80) cc_final: 0.6153 (m-80) REVERT: A 217 MET cc_start: 0.5782 (mtm) cc_final: 0.4495 (mtm) REVERT: A 232 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7171 (t70) REVERT: A 233 GLU cc_start: 0.7755 (pt0) cc_final: 0.7120 (mp0) REVERT: A 235 THR cc_start: 0.8594 (m) cc_final: 0.8286 (p) REVERT: A 268 MET cc_start: 0.8851 (tpp) cc_final: 0.8634 (tpp) REVERT: A 754 MET cc_start: 0.8225 (tmm) cc_final: 0.7604 (tmm) REVERT: A 789 ARG cc_start: 0.6286 (OUTLIER) cc_final: 0.6061 (ptp-170) REVERT: A 899 TYR cc_start: 0.7502 (m-80) cc_final: 0.7048 (m-80) REVERT: A 912 MET cc_start: 0.7278 (mmm) cc_final: 0.7025 (mtp) REVERT: A 921 GLN cc_start: 0.8721 (tp-100) cc_final: 0.8471 (tp-100) REVERT: A 1161 CYS cc_start: 0.8418 (p) cc_final: 0.8019 (p) REVERT: A 1173 ARG cc_start: 0.8708 (tpp80) cc_final: 0.8281 (tpp80) REVERT: A 1251 ILE cc_start: 0.8702 (mm) cc_final: 0.8284 (tt) REVERT: D 36 GLU cc_start: 0.6837 (tt0) cc_final: 0.6070 (tp30) REVERT: D 64 ASN cc_start: 0.9179 (t0) cc_final: 0.8798 (m110) REVERT: D 75 HIS cc_start: 0.8001 (m-70) cc_final: 0.7346 (m-70) REVERT: D 146 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7304 (tm-30) outliers start: 68 outliers final: 31 residues processed: 313 average time/residue: 0.0752 time to fit residues: 35.9640 Evaluate side-chains 241 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 207 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 1040 THR 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 111 ASN Chi-restraints excluded: chain D residue 113 LEU 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: 7.9990 chunk 66 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 chunk 37 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** 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** D 111 ASN D 129 GLN D 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.098986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.076793 restraints weight = 33239.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.079123 restraints weight = 17332.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.080624 restraints weight = 11363.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.081572 restraints weight = 8652.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.082143 restraints weight = 7278.198| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10901 Z= 0.179 Angle : 0.883 12.371 14910 Z= 0.413 Chirality : 0.050 0.290 1736 Planarity : 0.005 0.045 1851 Dihedral : 12.072 100.416 2057 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 5.87 % Allowed : 22.52 % Favored : 71.60 % 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: -0.87 (0.23), residues: 1297 helix: 0.47 (0.20), residues: 619 sheet: -0.96 (0.39), residues: 150 loop : -1.70 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 116 TYR 0.029 0.002 TYR A1225 PHE 0.020 0.002 PHE A 503 TRP 0.021 0.002 TRP D 141 HIS 0.005 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00392 (10863) covalent geometry : angle 0.83376 (14814) SS BOND : bond 0.00918 ( 18) SS BOND : angle 2.70511 ( 36) hydrogen bonds : bond 0.04807 ( 529) hydrogen bonds : angle 5.29522 ( 1506) link_BETA1-3 : bond 0.02044 ( 1) link_BETA1-3 : angle 6.12036 ( 3) link_BETA1-4 : bond 0.01174 ( 5) link_BETA1-4 : angle 4.00827 ( 15) link_NAG-ASN : bond 0.00725 ( 14) link_NAG-ASN : angle 4.14322 ( 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 283 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 216 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7911 (ptmm) REVERT: A 78 ARG cc_start: 0.7823 (tpt-90) cc_final: 0.7559 (mmm-85) REVERT: A 232 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7184 (t70) REVERT: A 233 GLU cc_start: 0.7798 (pt0) cc_final: 0.7254 (mp0) REVERT: A 235 THR cc_start: 0.8564 (m) cc_final: 0.8181 (p) REVERT: A 487 TYR cc_start: 0.8495 (m-80) cc_final: 0.8226 (m-80) REVERT: A 596 ASN cc_start: 0.8071 (t0) cc_final: 0.7766 (t0) REVERT: A 754 MET cc_start: 0.8167 (tmm) cc_final: 0.7277 (tmm) REVERT: A 789 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.5954 (ptp-170) REVERT: A 899 TYR cc_start: 0.7517 (m-80) cc_final: 0.6879 (m-80) REVERT: A 921 GLN cc_start: 0.8752 (tp-100) cc_final: 0.8427 (tp-100) REVERT: A 1102 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8515 (mm) REVERT: A 1122 TRP cc_start: 0.6434 (m-10) cc_final: 0.5916 (m100) REVERT: A 1173 ARG cc_start: 0.8772 (tpp80) cc_final: 0.8324 (tpp80) REVERT: D 36 GLU cc_start: 0.6947 (tt0) cc_final: 0.6643 (tp30) REVERT: D 64 ASN cc_start: 0.9353 (t0) cc_final: 0.8850 (m110) REVERT: D 75 HIS cc_start: 0.8400 (m-70) cc_final: 0.8169 (m90) REVERT: D 104 ASP cc_start: 0.9246 (m-30) cc_final: 0.8609 (p0) REVERT: D 146 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7087 (tm-30) outliers start: 67 outliers final: 43 residues processed: 264 average time/residue: 0.0812 time to fit residues: 32.6425 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 : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 74 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 232 ASP Chi-restraints excluded: chain A residue 242 ASP 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 360 PHE 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 735 MET Chi-restraints excluded: chain A residue 738 SER 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 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 1099 ILE Chi-restraints excluded: chain A residue 1102 LEU 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 1158 VAL 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 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: 0.8980 chunk 22 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.097728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.075393 restraints weight = 33249.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.077662 restraints weight = 17522.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.079148 restraints weight = 11564.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.080061 restraints weight = 8807.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.080680 restraints weight = 7438.014| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10901 Z= 0.198 Angle : 0.871 12.088 14910 Z= 0.407 Chirality : 0.048 0.293 1736 Planarity : 0.005 0.043 1851 Dihedral : 10.973 96.580 2053 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 5.70 % Allowed : 23.93 % Favored : 70.38 % 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: -0.70 (0.23), residues: 1297 helix: 0.60 (0.20), residues: 616 sheet: -0.96 (0.39), residues: 151 loop : -1.57 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1183 TYR 0.025 0.002 TYR D 109 PHE 0.018 0.002 PHE A 632 TRP 0.017 0.002 TRP D 141 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd covalent geometry : bond 0.00437 (10863) covalent geometry : angle 0.82447 (14814) SS BOND : bond 0.00438 ( 18) SS BOND : angle 2.68913 ( 36) hydrogen bonds : bond 0.04794 ( 529) hydrogen bonds : angle 5.26397 ( 1506) link_BETA1-3 : bond 0.01595 ( 1) link_BETA1-3 : angle 5.75840 ( 3) link_BETA1-4 : bond 0.01073 ( 5) link_BETA1-4 : angle 3.92759 ( 15) link_NAG-ASN : bond 0.00624 ( 14) link_NAG-ASN : angle 3.95019 ( 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 272 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 207 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7915 (tpt-90) cc_final: 0.7591 (mmm-85) REVERT: A 147 TYR cc_start: 0.7151 (m-80) cc_final: 0.6620 (m-80) REVERT: A 233 GLU cc_start: 0.7931 (pt0) cc_final: 0.7010 (mp0) REVERT: A 487 TYR cc_start: 0.8516 (m-80) cc_final: 0.8274 (m-80) REVERT: A 754 MET cc_start: 0.8189 (tmm) cc_final: 0.7131 (tmm) REVERT: A 789 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.5810 (tmt170) REVERT: A 899 TYR cc_start: 0.7536 (m-80) cc_final: 0.6840 (m-80) REVERT: A 912 MET cc_start: 0.8509 (mpp) cc_final: 0.7783 (mtp) REVERT: A 921 GLN cc_start: 0.8834 (tp-100) cc_final: 0.8512 (tp-100) REVERT: A 1122 TRP cc_start: 0.6476 (m-10) cc_final: 0.5934 (m100) REVERT: A 1159 MET cc_start: 0.8739 (tmm) cc_final: 0.8515 (ttp) REVERT: A 1173 ARG cc_start: 0.8797 (tpp80) cc_final: 0.8384 (tpp80) REVERT: A 1229 TYR cc_start: 0.8059 (m-10) cc_final: 0.7810 (m-10) REVERT: D 25 LYS cc_start: 0.7584 (mtpt) cc_final: 0.7334 (mtmt) REVERT: D 36 GLU cc_start: 0.6925 (tt0) cc_final: 0.6096 (tp30) REVERT: D 64 ASN cc_start: 0.9295 (t0) cc_final: 0.8876 (m110) REVERT: D 75 HIS cc_start: 0.8356 (m-70) cc_final: 0.8102 (m90) REVERT: D 104 ASP cc_start: 0.9254 (m-30) cc_final: 0.8621 (p0) REVERT: D 112 LYS cc_start: 0.8278 (tptt) cc_final: 0.7581 (mmtm) REVERT: D 146 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7374 (tm-30) outliers start: 65 outliers final: 47 residues processed: 247 average time/residue: 0.0783 time to fit residues: 29.5996 Evaluate side-chains 244 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 109 CYS Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 242 ASP 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 360 PHE 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 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 862 GLN 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 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 1106 LEU 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 1205 THR 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: 2.9990 chunk 78 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.096288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.074459 restraints weight = 33298.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.076593 restraints weight = 17973.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.077999 restraints weight = 12045.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.078875 restraints weight = 9276.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.079466 restraints weight = 7864.776| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 10901 Z= 0.233 Angle : 0.884 11.914 14910 Z= 0.418 Chirality : 0.049 0.305 1736 Planarity : 0.005 0.045 1851 Dihedral : 10.433 94.702 2050 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 6.13 % Allowed : 24.63 % Favored : 69.24 % 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: -0.63 (0.23), residues: 1297 helix: 0.65 (0.21), residues: 617 sheet: -0.86 (0.41), residues: 147 loop : -1.54 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1183 TYR 0.022 0.002 TYR A1225 PHE 0.019 0.002 PHE A 587 TRP 0.014 0.002 TRP D 141 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd covalent geometry : bond 0.00515 (10863) covalent geometry : angle 0.83968 (14814) SS BOND : bond 0.00440 ( 18) SS BOND : angle 2.64408 ( 36) hydrogen bonds : bond 0.04881 ( 529) hydrogen bonds : angle 5.32546 ( 1506) link_BETA1-3 : bond 0.01481 ( 1) link_BETA1-3 : angle 5.47331 ( 3) link_BETA1-4 : bond 0.01286 ( 5) link_BETA1-4 : angle 3.91601 ( 15) link_NAG-ASN : bond 0.00581 ( 14) link_NAG-ASN : angle 3.92134 ( 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 268 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 198 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7969 (tpt-90) cc_final: 0.7592 (mmm-85) REVERT: A 233 GLU cc_start: 0.8006 (pt0) cc_final: 0.7047 (mp0) REVERT: A 381 TRP cc_start: 0.7909 (t-100) cc_final: 0.7698 (t-100) REVERT: A 487 TYR cc_start: 0.8523 (m-80) cc_final: 0.8241 (m-80) REVERT: A 754 MET cc_start: 0.8334 (tmm) cc_final: 0.7165 (tmm) REVERT: A 789 ARG cc_start: 0.5689 (OUTLIER) cc_final: 0.5405 (ptp-170) REVERT: A 921 GLN cc_start: 0.8817 (tp-100) cc_final: 0.8549 (tp-100) REVERT: A 1102 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8635 (mm) REVERT: A 1122 TRP cc_start: 0.6498 (OUTLIER) cc_final: 0.5911 (m100) REVERT: A 1159 MET cc_start: 0.8875 (tmm) cc_final: 0.8463 (ttp) REVERT: A 1173 ARG cc_start: 0.8745 (tpp80) cc_final: 0.8317 (tpp80) REVERT: A 1179 MET cc_start: 0.6258 (mmt) cc_final: 0.5926 (mmt) REVERT: A 1217 LYS cc_start: 0.7568 (tppp) cc_final: 0.6255 (tptt) REVERT: D 36 GLU cc_start: 0.7033 (tt0) cc_final: 0.6051 (tp30) REVERT: D 64 ASN cc_start: 0.9243 (t0) cc_final: 0.8872 (m110) REVERT: D 75 HIS cc_start: 0.8296 (m-70) cc_final: 0.8034 (m90) REVERT: D 104 ASP cc_start: 0.9225 (m-30) cc_final: 0.8616 (p0) REVERT: D 146 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7606 (tm-30) outliers start: 70 outliers final: 49 residues processed: 245 average time/residue: 0.0770 time to fit residues: 29.3671 Evaluate side-chains 235 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 182 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 105 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 263 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 360 PHE 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 613 LEU 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 739 SER Chi-restraints excluded: chain A residue 778 CYS 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 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 1086 VAL Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1102 LEU 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: 9.9990 chunk 4 optimal weight: 0.0970 chunk 97 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 90 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 0.0070 chunk 111 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.098240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.076468 restraints weight = 33146.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.078705 restraints weight = 17628.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.080164 restraints weight = 11681.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.081078 restraints weight = 8938.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.081687 restraints weight = 7547.997| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10901 Z= 0.149 Angle : 0.844 15.740 14910 Z= 0.391 Chirality : 0.047 0.300 1736 Planarity : 0.004 0.042 1851 Dihedral : 9.837 89.305 2046 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 5.52 % Allowed : 27.78 % Favored : 66.70 % 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: -0.56 (0.23), residues: 1297 helix: 0.74 (0.21), residues: 614 sheet: -0.75 (0.41), residues: 147 loop : -1.55 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1183 TYR 0.022 0.002 TYR A1225 PHE 0.021 0.001 PHE A 632 TRP 0.012 0.002 TRP A 27 HIS 0.005 0.001 HIS A1042 Details of bonding type rmsd covalent geometry : bond 0.00326 (10863) covalent geometry : angle 0.80213 (14814) SS BOND : bond 0.00365 ( 18) SS BOND : angle 2.45334 ( 36) hydrogen bonds : bond 0.04613 ( 529) hydrogen bonds : angle 5.15450 ( 1506) link_BETA1-3 : bond 0.00962 ( 1) link_BETA1-3 : angle 5.06598 ( 3) link_BETA1-4 : bond 0.01177 ( 5) link_BETA1-4 : angle 3.86728 ( 15) link_NAG-ASN : bond 0.00613 ( 14) link_NAG-ASN : angle 3.71260 ( 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 268 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 205 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8039 (tpt-90) cc_final: 0.7594 (mmm160) REVERT: A 109 CYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7477 (t) REVERT: A 147 TYR cc_start: 0.7170 (m-80) cc_final: 0.6638 (m-80) REVERT: A 193 MET cc_start: 0.9144 (tpp) cc_final: 0.8873 (tpp) REVERT: A 233 GLU cc_start: 0.8031 (pt0) cc_final: 0.7011 (mp0) REVERT: A 487 TYR cc_start: 0.8403 (m-80) cc_final: 0.8157 (m-80) REVERT: A 754 MET cc_start: 0.8195 (tmm) cc_final: 0.7235 (tmm) REVERT: A 789 ARG cc_start: 0.5562 (OUTLIER) cc_final: 0.5232 (ptp-170) REVERT: A 921 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8420 (tp-100) REVERT: A 1102 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8573 (mm) REVERT: A 1122 TRP cc_start: 0.6421 (m-10) cc_final: 0.5919 (m100) REVERT: A 1173 ARG cc_start: 0.8696 (tpp80) cc_final: 0.8273 (tpp80) REVERT: A 1179 MET cc_start: 0.6252 (mmt) cc_final: 0.5965 (mmt) REVERT: A 1217 LYS cc_start: 0.7599 (tppp) cc_final: 0.6235 (tptt) REVERT: A 1225 TYR cc_start: 0.7953 (m-80) cc_final: 0.7726 (m-80) REVERT: D 36 GLU cc_start: 0.7277 (tt0) cc_final: 0.6277 (tp30) REVERT: D 64 ASN cc_start: 0.9276 (t0) cc_final: 0.8895 (m110) REVERT: D 75 HIS cc_start: 0.8247 (m-70) cc_final: 0.7971 (m90) REVERT: D 104 ASP cc_start: 0.9179 (m-30) cc_final: 0.8545 (p0) REVERT: D 146 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7480 (tm-30) outliers start: 63 outliers final: 47 residues processed: 249 average time/residue: 0.0705 time to fit residues: 27.3954 Evaluate side-chains 240 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 63 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 109 CYS 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 242 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 360 PHE 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 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 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 1102 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 27 CYS Chi-restraints excluded: chain D residue 111 ASN Chi-restraints excluded: chain D residue 146 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 5 optimal weight: 7.9990 chunk 123 optimal weight: 0.0370 chunk 49 optimal weight: 0.5980 chunk 126 optimal weight: 9.9990 chunk 32 optimal weight: 0.1980 chunk 62 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.099718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.078131 restraints weight = 32742.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.080434 restraints weight = 17457.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.081900 restraints weight = 11563.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.082821 restraints weight = 8832.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.083451 restraints weight = 7457.015| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10901 Z= 0.143 Angle : 0.849 14.906 14910 Z= 0.391 Chirality : 0.047 0.299 1736 Planarity : 0.004 0.041 1851 Dihedral : 9.327 85.187 2046 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.21 % Allowed : 29.10 % Favored : 66.70 % 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: -0.48 (0.23), residues: 1297 helix: 0.75 (0.21), residues: 613 sheet: -0.59 (0.42), residues: 145 loop : -1.47 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1183 TYR 0.018 0.001 TYR A 594 PHE 0.018 0.001 PHE A 632 TRP 0.014 0.001 TRP A1143 HIS 0.006 0.001 HIS A 897 Details of bonding type rmsd covalent geometry : bond 0.00301 (10863) covalent geometry : angle 0.81002 (14814) SS BOND : bond 0.00380 ( 18) SS BOND : angle 2.49280 ( 36) hydrogen bonds : bond 0.04433 ( 529) hydrogen bonds : angle 5.07225 ( 1506) link_BETA1-3 : bond 0.00812 ( 1) link_BETA1-3 : angle 4.67121 ( 3) link_BETA1-4 : bond 0.01141 ( 5) link_BETA1-4 : angle 3.81879 ( 15) link_NAG-ASN : bond 0.00639 ( 14) link_NAG-ASN : angle 3.49872 ( 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 267 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 219 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8027 (tpt-90) cc_final: 0.7781 (mmm-85) REVERT: A 147 TYR cc_start: 0.7184 (m-80) cc_final: 0.6619 (m-80) REVERT: A 233 GLU cc_start: 0.8021 (pt0) cc_final: 0.6935 (mp0) REVERT: A 487 TYR cc_start: 0.8393 (m-80) cc_final: 0.8184 (m-80) REVERT: A 754 MET cc_start: 0.8147 (tmm) cc_final: 0.7050 (tmm) REVERT: A 789 ARG cc_start: 0.5594 (OUTLIER) cc_final: 0.5177 (ptp-170) REVERT: A 912 MET cc_start: 0.7816 (mpp) cc_final: 0.7465 (mtp) REVERT: A 921 GLN cc_start: 0.8743 (tp-100) cc_final: 0.8360 (tp-100) REVERT: A 1102 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8574 (mm) REVERT: A 1122 TRP cc_start: 0.6214 (m-10) cc_final: 0.5899 (m100) REVERT: A 1160 SER cc_start: 0.9122 (m) cc_final: 0.8734 (m) REVERT: A 1173 ARG cc_start: 0.8668 (tpp80) cc_final: 0.8353 (tpt-90) REVERT: A 1179 MET cc_start: 0.6207 (mmt) cc_final: 0.5918 (mmt) REVERT: A 1217 LYS cc_start: 0.7644 (tppp) cc_final: 0.6329 (tptt) REVERT: A 1223 ILE cc_start: 0.8577 (mt) cc_final: 0.8293 (mt) REVERT: D 36 GLU cc_start: 0.7321 (tt0) cc_final: 0.6391 (tp30) REVERT: D 64 ASN cc_start: 0.9292 (t0) cc_final: 0.8951 (m110) REVERT: D 75 HIS cc_start: 0.8146 (m-70) cc_final: 0.7701 (m90) outliers start: 48 outliers final: 37 residues processed: 254 average time/residue: 0.0755 time to fit residues: 29.6909 Evaluate side-chains 232 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 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 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 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 662 LEU 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 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 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 1102 LEU 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 D residue 27 CYS 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: 4.9990 chunk 112 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 1 optimal weight: 20.0000 chunk 103 optimal weight: 0.0770 chunk 4 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 GLN ** 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 = 0.3676 r_free = 0.3676 target = 0.099073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.077418 restraints weight = 32729.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.079775 restraints weight = 17100.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.081261 restraints weight = 11092.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.082233 restraints weight = 8385.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.082793 restraints weight = 6971.945| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10901 Z= 0.149 Angle : 0.829 14.560 14910 Z= 0.386 Chirality : 0.047 0.302 1736 Planarity : 0.004 0.039 1851 Dihedral : 8.978 81.998 2043 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.82 % Allowed : 29.71 % Favored : 65.47 % 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: -0.47 (0.24), residues: 1297 helix: 0.68 (0.21), residues: 620 sheet: -0.46 (0.43), residues: 146 loop : -1.44 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1183 TYR 0.023 0.001 TYR D 109 PHE 0.025 0.001 PHE A 769 TRP 0.045 0.002 TRP A 381 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd covalent geometry : bond 0.00329 (10863) covalent geometry : angle 0.79344 (14814) SS BOND : bond 0.00352 ( 18) SS BOND : angle 2.05451 ( 36) hydrogen bonds : bond 0.04354 ( 529) hydrogen bonds : angle 5.11550 ( 1506) link_BETA1-3 : bond 0.00813 ( 1) link_BETA1-3 : angle 4.45200 ( 3) link_BETA1-4 : bond 0.01136 ( 5) link_BETA1-4 : angle 3.88539 ( 15) link_NAG-ASN : bond 0.00565 ( 14) link_NAG-ASN : angle 3.43030 ( 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 256 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8081 (tpt-90) cc_final: 0.7800 (mmm-85) REVERT: A 147 TYR cc_start: 0.7203 (m-80) cc_final: 0.6547 (m-80) REVERT: A 193 MET cc_start: 0.9231 (tpp) cc_final: 0.8995 (tpp) REVERT: A 487 TYR cc_start: 0.8489 (m-80) cc_final: 0.8227 (m-80) REVERT: A 754 MET cc_start: 0.8089 (tmm) cc_final: 0.7018 (tmm) REVERT: A 789 ARG cc_start: 0.5748 (OUTLIER) cc_final: 0.5158 (ptm160) REVERT: A 912 MET cc_start: 0.7870 (mpp) cc_final: 0.7553 (mtp) REVERT: A 1102 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8557 (mm) REVERT: A 1122 TRP cc_start: 0.6390 (m-10) cc_final: 0.5999 (m100) REVERT: A 1160 SER cc_start: 0.9288 (m) cc_final: 0.8991 (m) REVERT: A 1173 ARG cc_start: 0.8789 (tpp80) cc_final: 0.8227 (tpp80) REVERT: A 1179 MET cc_start: 0.6220 (mmt) cc_final: 0.5936 (mmt) REVERT: A 1194 MET cc_start: 0.8735 (mmm) cc_final: 0.8076 (tpt) REVERT: A 1223 ILE cc_start: 0.8501 (mt) cc_final: 0.8203 (mt) REVERT: D 36 GLU cc_start: 0.7328 (tt0) cc_final: 0.6915 (tp30) REVERT: D 64 ASN cc_start: 0.9248 (t0) cc_final: 0.8952 (m-40) REVERT: D 75 HIS cc_start: 0.8148 (m-70) cc_final: 0.7654 (m90) REVERT: D 112 LYS cc_start: 0.8162 (tptt) cc_final: 0.7594 (mmtm) outliers start: 55 outliers final: 41 residues processed: 242 average time/residue: 0.0750 time to fit residues: 28.2693 Evaluate side-chains 237 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 CYS Chi-restraints excluded: chain A residue 63 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 293 TYR 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 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 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 909 CYS 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 1102 LEU 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 A residue 1254 SER Chi-restraints excluded: chain D residue 27 CYS 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: 2.9990 chunk 38 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 117 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 GLN ** 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 = 0.3688 r_free = 0.3688 target = 0.099786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.078194 restraints weight = 33019.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.080605 restraints weight = 16984.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.082144 restraints weight = 10979.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.083143 restraints weight = 8237.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.083748 restraints weight = 6825.058| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10901 Z= 0.143 Angle : 0.860 14.504 14910 Z= 0.396 Chirality : 0.046 0.296 1736 Planarity : 0.004 0.039 1851 Dihedral : 8.688 77.548 2043 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.29 % Allowed : 30.15 % Favored : 65.56 % 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: -0.52 (0.23), residues: 1297 helix: 0.63 (0.21), residues: 619 sheet: -0.36 (0.43), residues: 143 loop : -1.46 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1173 TYR 0.021 0.001 TYR A1229 PHE 0.021 0.001 PHE A 194 TRP 0.023 0.002 TRP A 381 HIS 0.005 0.001 HIS A1042 Details of bonding type rmsd covalent geometry : bond 0.00312 (10863) covalent geometry : angle 0.82587 (14814) SS BOND : bond 0.00300 ( 18) SS BOND : angle 2.18622 ( 36) hydrogen bonds : bond 0.04295 ( 529) hydrogen bonds : angle 5.13637 ( 1506) link_BETA1-3 : bond 0.00783 ( 1) link_BETA1-3 : angle 4.16832 ( 3) link_BETA1-4 : bond 0.01077 ( 5) link_BETA1-4 : angle 3.87580 ( 15) link_NAG-ASN : bond 0.00587 ( 14) link_NAG-ASN : angle 3.40184 ( 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 255 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 206 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 TYR cc_start: 0.7211 (m-80) cc_final: 0.6729 (m-80) REVERT: A 162 ASP cc_start: 0.7923 (m-30) cc_final: 0.7431 (m-30) REVERT: A 487 TYR cc_start: 0.8451 (m-80) cc_final: 0.8210 (m-80) REVERT: A 754 MET cc_start: 0.8244 (tmm) cc_final: 0.7156 (tmm) REVERT: A 864 LEU cc_start: 0.7956 (pt) cc_final: 0.7743 (pp) REVERT: A 912 MET cc_start: 0.7646 (mpp) cc_final: 0.7342 (mtp) REVERT: A 1102 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8552 (mm) REVERT: A 1122 TRP cc_start: 0.6350 (m-10) cc_final: 0.5970 (m100) REVERT: A 1173 ARG cc_start: 0.8653 (tpp80) cc_final: 0.8288 (tpp80) REVERT: A 1179 MET cc_start: 0.6257 (mmt) cc_final: 0.6014 (mmt) REVERT: A 1194 MET cc_start: 0.8745 (mmm) cc_final: 0.8104 (tpt) REVERT: A 1217 LYS cc_start: 0.6283 (mttp) cc_final: 0.5573 (tptt) REVERT: A 1223 ILE cc_start: 0.8529 (mt) cc_final: 0.8222 (mt) REVERT: D 36 GLU cc_start: 0.7345 (tt0) cc_final: 0.6371 (tp30) REVERT: D 55 TYR cc_start: 0.7060 (m-80) cc_final: 0.6688 (m-80) REVERT: D 64 ASN cc_start: 0.9247 (t0) cc_final: 0.8968 (m-40) REVERT: D 75 HIS cc_start: 0.8078 (m-70) cc_final: 0.7606 (m90) outliers start: 49 outliers final: 42 residues processed: 242 average time/residue: 0.0756 time to fit residues: 28.5880 Evaluate side-chains 229 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 293 TYR Chi-restraints excluded: chain A residue 360 PHE 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 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 739 SER 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 973 ASP Chi-restraints excluded: chain A residue 976 CYS 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 1102 LEU 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 A residue 1254 SER 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 81 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 GLN ** A1222 GLN ** 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 = 0.3668 r_free = 0.3668 target = 0.098538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.077190 restraints weight = 32923.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.079419 restraints weight = 17619.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.080877 restraints weight = 11700.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.081776 restraints weight = 8897.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.082323 restraints weight = 7471.133| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10901 Z= 0.170 Angle : 0.851 14.187 14910 Z= 0.395 Chirality : 0.047 0.306 1736 Planarity : 0.005 0.088 1851 Dihedral : 8.571 75.528 2039 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.86 % Allowed : 30.94 % Favored : 65.21 % 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: -0.45 (0.23), residues: 1297 helix: 0.72 (0.21), residues: 612 sheet: -0.35 (0.43), residues: 144 loop : -1.44 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 989 TYR 0.024 0.002 TYR D 109 PHE 0.024 0.002 PHE A 194 TRP 0.021 0.002 TRP A1143 HIS 0.007 0.001 HIS A1239 Details of bonding type rmsd covalent geometry : bond 0.00380 (10863) covalent geometry : angle 0.81661 (14814) SS BOND : bond 0.00284 ( 18) SS BOND : angle 2.12591 ( 36) hydrogen bonds : bond 0.04363 ( 529) hydrogen bonds : angle 5.16177 ( 1506) link_BETA1-3 : bond 0.00829 ( 1) link_BETA1-3 : angle 4.13184 ( 3) link_BETA1-4 : bond 0.01071 ( 5) link_BETA1-4 : angle 3.89135 ( 15) link_NAG-ASN : bond 0.00532 ( 14) link_NAG-ASN : angle 3.39696 ( 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 240 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 196 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 TYR cc_start: 0.7209 (m-80) cc_final: 0.6727 (m-80) REVERT: A 487 TYR cc_start: 0.8489 (m-80) cc_final: 0.8213 (m-80) REVERT: A 754 MET cc_start: 0.8206 (tmm) cc_final: 0.7067 (tmm) REVERT: A 864 LEU cc_start: 0.8031 (pt) cc_final: 0.7637 (pp) REVERT: A 912 MET cc_start: 0.7731 (mpp) cc_final: 0.7437 (mtm) REVERT: A 1102 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8578 (mm) REVERT: A 1122 TRP cc_start: 0.6396 (m-10) cc_final: 0.6120 (m100) REVERT: A 1173 ARG cc_start: 0.8658 (tpp80) cc_final: 0.8298 (tpp80) REVERT: A 1219 GLN cc_start: 0.8232 (mt0) cc_final: 0.7830 (mt0) REVERT: A 1223 ILE cc_start: 0.8577 (mt) cc_final: 0.8287 (mt) REVERT: D 64 ASN cc_start: 0.9208 (t0) cc_final: 0.8935 (m-40) REVERT: D 75 HIS cc_start: 0.8108 (m-70) cc_final: 0.7621 (m90) REVERT: D 141 TRP cc_start: 0.6582 (p-90) cc_final: 0.5507 (p-90) outliers start: 44 outliers final: 43 residues processed: 227 average time/residue: 0.0756 time to fit residues: 26.8472 Evaluate side-chains 236 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 293 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 PHE 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 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 838 VAL Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 976 CYS 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 1102 LEU 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 A residue 1254 SER 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: 5.9990 chunk 45 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 118 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.099792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.078127 restraints weight = 32871.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.080524 restraints weight = 17046.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.082081 restraints weight = 11073.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.083055 restraints weight = 8313.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.083666 restraints weight = 6914.514| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10901 Z= 0.146 Angle : 0.858 15.567 14910 Z= 0.395 Chirality : 0.046 0.300 1736 Planarity : 0.005 0.091 1851 Dihedral : 8.428 71.068 2039 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.86 % Allowed : 31.64 % Favored : 64.50 % 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: -0.44 (0.23), residues: 1297 helix: 0.72 (0.21), residues: 612 sheet: -0.31 (0.43), residues: 142 loop : -1.44 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 579 TYR 0.029 0.001 TYR A1229 PHE 0.029 0.001 PHE A 760 TRP 0.021 0.002 TRP A1143 HIS 0.007 0.001 HIS A1239 Details of bonding type rmsd covalent geometry : bond 0.00322 (10863) covalent geometry : angle 0.82549 (14814) SS BOND : bond 0.00257 ( 18) SS BOND : angle 1.92716 ( 36) hydrogen bonds : bond 0.04349 ( 529) hydrogen bonds : angle 5.11206 ( 1506) link_BETA1-3 : bond 0.00790 ( 1) link_BETA1-3 : angle 3.94520 ( 3) link_BETA1-4 : bond 0.01073 ( 5) link_BETA1-4 : angle 3.84822 ( 15) link_NAG-ASN : bond 0.00568 ( 14) link_NAG-ASN : angle 3.34957 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1904.53 seconds wall clock time: 33 minutes 30.56 seconds (2010.56 seconds total)