Starting phenix.real_space_refine on Tue Dec 31 10:26:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w5r_21545/12_2024/6w5r_21545.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5r_21545/12_2024/6w5r_21545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6w5r_21545/12_2024/6w5r_21545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5r_21545/12_2024/6w5r_21545.map" model { file = "/net/cci-nas-00/data/ceres_data/6w5r_21545/12_2024/6w5r_21545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5r_21545/12_2024/6w5r_21545.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 6665 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 75 5.16 5 C 6223 2.51 5 N 1525 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9629 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9341 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1130} Chain breaks: 2 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 154 Unusual residues: {'CLR': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.99, per 1000 atoms: 0.62 Number of scatterers: 9629 At special positions: 0 Unit cell: (105.83, 93.576, 155.96, 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 75 16.00 O 1806 8.00 N 1525 7.00 C 6223 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.08 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=2.05 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.02 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.02 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.03 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.03 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=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG E 2 " - " MAN E 3 " BETA1-3 " NAG D 2 " - " BMA D 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1403 " - " ASN A 158 " " NAG A1404 " - " ASN A 452 " " NAG A1405 " - " ASN A 459 " " NAG A1408 " - " ASN A 524 " " NAG A1412 " - " ASN A 598 " " NAG A1413 " - " ASN A 916 " " NAG A1417 " - " ASN A 961 " " NAG A1418 " - " ASN A 968 " " NAG A1419 " - " ASN A1064 " " NAG B 1 " - " ASN A 222 " " NAG C 1 " - " ASN A 478 " " NAG D 1 " - " ASN A 557 " " NAG E 1 " - " ASN A 931 " Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.4 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 57.4% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.549A pdb=" N VAL A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.814A pdb=" N THR A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.825A pdb=" N GLU A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 149 through 161 removed outlier: 3.631A pdb=" N ALA A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.576A pdb=" N LEU A 175 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 266 through 294 removed outlier: 3.580A pdb=" N VAL A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TRP A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 349 removed outlier: 3.844A pdb=" N PHE A 331 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N CYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 366 removed outlier: 3.779A pdb=" N VAL A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.656A pdb=" N VAL A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 382 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 436 through 453 removed outlier: 3.971A 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 496 Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.899A pdb=" N ARG A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 545 Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.677A pdb=" N ALA A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 593 removed outlier: 3.932A pdb=" N GLU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 617 Processing helix chain 'A' and resid 620 through 639 removed outlier: 4.165A pdb=" N ILE A 626 " --> pdb=" O PHE A 622 " (cutoff:3.500A) 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 removed outlier: 3.540A pdb=" N ASP A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 749 Proline residue: A 733 - end of helix Processing helix chain 'A' and resid 754 through 792 removed outlier: 4.715A pdb=" N VAL A 780 " --> pdb=" O ILE A 776 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 824 through 830 removed outlier: 3.987A pdb=" N LEU A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 852 Processing helix chain 'A' and resid 853 through 856 removed outlier: 3.552A pdb=" N VAL A 856 " --> pdb=" O LEU A 853 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 853 through 856' Processing helix chain 'A' and resid 870 through 883 removed outlier: 4.200A 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 942 through 951 Processing helix chain 'A' and resid 993 through 1004 Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1047 through 1070 removed outlier: 3.892A pdb=" N GLY A1070 " --> pdb=" O THR A1066 " (cutoff:3.500A) 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 1145 removed outlier: 3.869A pdb=" N ALA A1124 " --> pdb=" O GLU A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1177 removed outlier: 3.882A pdb=" N GLY A1162 " --> pdb=" O VAL A1158 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL A1165 " --> pdb=" O CYS A1161 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1182 through 1202 removed outlier: 4.301A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A1200 " --> pdb=" O SER A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1214 Processing helix chain 'A' and resid 1218 through 1225 Processing helix chain 'A' and resid 1225 through 1252 Proline residue: A1245 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.831A pdb=" N CYS A 42 " --> pdb=" O TYR A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 129 removed outlier: 7.350A pdb=" N LEU A 121 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR A 146 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A 123 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU A 144 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ALA A 125 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A 142 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 127 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N THR A 206 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LEU A 144 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL A 208 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TYR A 146 " --> pdb=" O VAL A 208 " (cutoff:3.500A) 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 1039 through 1041 Processing sheet with id=AA6, first strand: chain 'A' and resid 1023 through 1026 removed outlier: 5.993A pdb=" N ASN A1024 " --> pdb=" O GLY A1034 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A1032 " --> pdb=" O LEU A1026 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1374 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: 3.20 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1938 1.33 - 1.46: 2913 1.46 - 1.59: 4918 1.59 - 1.72: 4 1.72 - 1.85: 103 Bond restraints: 9876 Sorted by residual: bond pdb=" C THR A 983 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 1.335 1.443 -0.109 1.28e-02 6.10e+03 7.24e+01 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.572 -0.166 2.00e-02 2.50e+03 6.88e+01 bond pdb=" C1 NAG A1413 " pdb=" O5 NAG A1413 " ideal model delta sigma weight residual 1.406 1.561 -0.155 2.00e-02 2.50e+03 5.99e+01 bond pdb=" C LEU A1244 " pdb=" N PRO A1245 " ideal model delta sigma weight residual 1.335 1.442 -0.107 1.38e-02 5.25e+03 5.96e+01 bond pdb=" C TYR A 423 " pdb=" N PRO A 424 " ideal model delta sigma weight residual 1.334 1.487 -0.153 2.34e-02 1.83e+03 4.28e+01 ... (remaining 9871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.11: 13199 6.11 - 12.21: 234 12.21 - 18.32: 17 18.32 - 24.42: 3 24.42 - 30.53: 1 Bond angle restraints: 13454 Sorted by residual: angle pdb=" N ASN A 70 " pdb=" CA ASN A 70 " pdb=" C ASN A 70 " ideal model delta sigma weight residual 110.80 80.27 30.53 2.13e+00 2.20e-01 2.05e+02 angle pdb=" C PRO A 48 " pdb=" N LYS A 49 " pdb=" CA LYS A 49 " ideal model delta sigma weight residual 120.49 134.59 -14.10 1.42e+00 4.96e-01 9.87e+01 angle pdb=" N VAL A 71 " pdb=" CA VAL A 71 " pdb=" C VAL A 71 " ideal model delta sigma weight residual 110.53 118.55 -8.02 9.40e-01 1.13e+00 7.28e+01 angle pdb=" N PRO A 939 " pdb=" CA PRO A 939 " pdb=" C PRO A 939 " ideal model delta sigma weight residual 113.53 124.66 -11.13 1.39e+00 5.18e-01 6.41e+01 angle pdb=" CA CYS A 177 " pdb=" CB CYS A 177 " pdb=" SG CYS A 177 " ideal model delta sigma weight residual 114.40 131.61 -17.21 2.30e+00 1.89e-01 5.60e+01 ... (remaining 13449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.96: 5772 26.96 - 53.93: 286 53.93 - 80.89: 43 80.89 - 107.86: 24 107.86 - 134.82: 10 Dihedral angle restraints: 6135 sinusoidal: 2655 harmonic: 3480 Sorted by residual: dihedral pdb=" CA SER A 473 " pdb=" C SER A 473 " pdb=" N PRO A 474 " pdb=" CA PRO A 474 " ideal model delta harmonic sigma weight residual 0.00 41.59 -41.59 0 5.00e+00 4.00e-02 6.92e+01 dihedral pdb=" CA ASN A 478 " pdb=" C ASN A 478 " pdb=" N CYS A 479 " pdb=" CA CYS A 479 " ideal model delta harmonic sigma weight residual 180.00 139.83 40.17 0 5.00e+00 4.00e-02 6.45e+01 dihedral pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " pdb=" SG CYS A 109 " pdb=" CB CYS A 109 " ideal model delta sinusoidal sigma weight residual -86.00 -21.36 -64.64 1 1.00e+01 1.00e-02 5.49e+01 ... (remaining 6132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.954: 1570 0.954 - 1.909: 2 1.909 - 2.863: 0 2.863 - 3.818: 0 3.818 - 4.772: 1 Chirality restraints: 1573 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 2.37 -4.77 2.00e-02 2.50e+03 5.69e+04 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-02 2.50e+03 6.85e+03 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.01 -1.39 2.00e-02 2.50e+03 4.84e+03 ... (remaining 1570 not shown) Planarity restraints: 1703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.316 2.00e-02 2.50e+03 2.69e-01 9.04e+02 pdb=" C7 NAG E 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.182 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.468 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " -0.086 2.00e-02 2.50e+03 7.12e-02 6.33e+01 pdb=" C7 NAG C 2 " 0.024 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " -0.065 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " 0.113 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 107 " 0.035 2.00e-02 2.50e+03 6.97e-02 4.85e+01 pdb=" C LEU A 107 " -0.121 2.00e-02 2.50e+03 pdb=" O LEU A 107 " 0.045 2.00e-02 2.50e+03 pdb=" N PHE A 108 " 0.041 2.00e-02 2.50e+03 ... (remaining 1700 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 109 2.62 - 3.19: 7763 3.19 - 3.76: 14485 3.76 - 4.33: 18982 4.33 - 4.90: 32224 Nonbonded interactions: 73563 Sorted by model distance: nonbonded pdb=" O4 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.053 3.040 nonbonded pdb=" O ASP A 508 " pdb=" OG1 THR A 511 " model vdw 2.328 3.040 nonbonded pdb=" OG SER A 366 " pdb=" OH TYR A 677 " model vdw 2.341 3.040 nonbonded pdb=" O SER A 970 " pdb=" OG SER A 970 " model vdw 2.349 3.040 nonbonded pdb=" O ALA A1192 " pdb=" OG SER A1196 " model vdw 2.359 3.040 ... (remaining 73558 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 'C' } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'E' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.100 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 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 : 0.015 0.173 9876 Z= 0.987 Angle : 2.102 30.531 13454 Z= 1.200 Chirality : 0.179 4.772 1573 Planarity : 0.014 0.269 1690 Dihedral : 17.453 134.819 3852 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.73 % Favored : 92.59 % Rotamer: Outliers : 3.86 % Allowed : 8.41 % Favored : 87.73 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.21), residues: 1188 helix: -1.43 (0.18), residues: 617 sheet: -2.14 (0.60), residues: 75 loop : -3.18 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP A 833 HIS 0.026 0.005 HIS A1042 PHE 0.054 0.007 PHE A 108 TYR 0.046 0.007 TYR A 157 ARG 0.019 0.002 ARG A 789 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 1.064 Fit side-chains REVERT: A 220 MET cc_start: 0.2696 (ppp) cc_final: 0.2254 (ptm) REVERT: A 272 MET cc_start: 0.6926 (mmp) cc_final: 0.6707 (mmp) REVERT: A 436 ASP cc_start: 0.6657 (OUTLIER) cc_final: 0.6396 (m-30) REVERT: A 622 PHE cc_start: 0.6364 (t80) cc_final: 0.5641 (m-10) REVERT: A 633 LEU cc_start: 0.8508 (tp) cc_final: 0.8301 (tp) REVERT: A 1089 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7533 (tp30) outliers start: 40 outliers final: 16 residues processed: 181 average time/residue: 0.1949 time to fit residues: 52.0571 Evaluate side-chains 115 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1145 TRP Chi-restraints excluded: chain A residue 1169 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 145 GLN A 185 ASN A 442 GLN A 465 GLN A 476 ASN A 581 GLN A 701 ASN A 707 GLN A 897 HIS A 905 GLN A 906 ASN A1016 HIS ** A1029 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN A1193 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9876 Z= 0.221 Angle : 0.847 12.010 13454 Z= 0.408 Chirality : 0.050 0.361 1573 Planarity : 0.005 0.044 1690 Dihedral : 13.235 92.163 1769 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.31 % Favored : 93.43 % Rotamer: Outliers : 3.19 % Allowed : 14.11 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.23), residues: 1188 helix: 0.04 (0.20), residues: 623 sheet: -1.37 (0.69), residues: 59 loop : -2.54 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 291 HIS 0.009 0.001 HIS A1029 PHE 0.023 0.002 PHE A 101 TYR 0.015 0.002 TYR A 146 ARG 0.005 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.912 Fit side-chains REVERT: A 145 GLN cc_start: 0.4838 (OUTLIER) cc_final: 0.4616 (pp30) REVERT: A 220 MET cc_start: 0.2365 (ppp) cc_final: 0.1547 (ptm) REVERT: A 436 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6575 (m-30) REVERT: A 622 PHE cc_start: 0.6552 (t80) cc_final: 0.5831 (m-10) REVERT: A 769 PHE cc_start: 0.8626 (t80) cc_final: 0.8333 (t80) REVERT: A 1114 MET cc_start: 0.6894 (tmm) cc_final: 0.6628 (tmm) REVERT: A 1133 MET cc_start: 0.7195 (ttm) cc_final: 0.6961 (mtp) REVERT: A 1137 ASN cc_start: 0.8173 (m-40) cc_final: 0.7921 (m110) REVERT: A 1159 MET cc_start: 0.7918 (ttm) cc_final: 0.7669 (ttp) REVERT: A 1197 SER cc_start: 0.8846 (m) cc_final: 0.8543 (t) outliers start: 33 outliers final: 15 residues processed: 146 average time/residue: 0.1894 time to fit residues: 41.4949 Evaluate side-chains 119 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1145 TRP Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1179 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 107 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 86 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN A 581 GLN A 596 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9876 Z= 0.185 Angle : 0.765 11.322 13454 Z= 0.367 Chirality : 0.047 0.309 1573 Planarity : 0.004 0.041 1690 Dihedral : 10.843 82.625 1752 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.40 % Favored : 93.43 % Rotamer: Outliers : 3.38 % Allowed : 14.88 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.24), residues: 1188 helix: 0.68 (0.21), residues: 625 sheet: -1.50 (0.58), residues: 71 loop : -2.29 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 291 HIS 0.007 0.001 HIS A1029 PHE 0.024 0.001 PHE A 101 TYR 0.012 0.001 TYR A 457 ARG 0.003 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 220 MET cc_start: 0.2850 (ppp) cc_final: 0.1922 (ptm) REVERT: A 288 PHE cc_start: 0.6465 (OUTLIER) cc_final: 0.5756 (t80) REVERT: A 436 ASP cc_start: 0.6641 (OUTLIER) cc_final: 0.6383 (m-30) REVERT: A 551 ASP cc_start: 0.8387 (p0) cc_final: 0.8140 (p0) REVERT: A 622 PHE cc_start: 0.6471 (t80) cc_final: 0.5762 (m-10) REVERT: A 858 ILE cc_start: 0.9064 (mm) cc_final: 0.8860 (mt) REVERT: A 1114 MET cc_start: 0.6789 (tmm) cc_final: 0.6427 (tmm) REVERT: A 1133 MET cc_start: 0.7126 (ttm) cc_final: 0.6920 (mtp) REVERT: A 1137 ASN cc_start: 0.8181 (m-40) cc_final: 0.7909 (m110) REVERT: A 1159 MET cc_start: 0.7970 (ttm) cc_final: 0.7757 (ttp) REVERT: A 1197 SER cc_start: 0.8849 (m) cc_final: 0.8528 (p) REVERT: A 1220 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.7076 (tp) outliers start: 35 outliers final: 20 residues processed: 146 average time/residue: 0.1642 time to fit residues: 37.3722 Evaluate side-chains 128 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1145 TRP Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 102 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9876 Z= 0.229 Angle : 0.734 10.495 13454 Z= 0.354 Chirality : 0.047 0.335 1573 Planarity : 0.004 0.049 1690 Dihedral : 9.579 68.360 1750 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.48 % Favored : 93.27 % Rotamer: Outliers : 4.15 % Allowed : 16.52 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1188 helix: 0.84 (0.21), residues: 634 sheet: -1.27 (0.62), residues: 71 loop : -2.06 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 833 HIS 0.006 0.001 HIS A1042 PHE 0.028 0.002 PHE A 769 TYR 0.021 0.001 TYR A 677 ARG 0.007 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6414 (OUTLIER) cc_final: 0.5634 (t80) REVERT: A 436 ASP cc_start: 0.6783 (OUTLIER) cc_final: 0.6529 (m-30) REVERT: A 622 PHE cc_start: 0.6375 (t80) cc_final: 0.5584 (m-10) REVERT: A 661 ILE cc_start: 0.7621 (mm) cc_final: 0.7316 (mm) REVERT: A 872 MET cc_start: 0.7947 (mmm) cc_final: 0.7719 (mmm) REVERT: A 1114 MET cc_start: 0.6834 (tmm) cc_final: 0.6320 (tmm) REVERT: A 1133 MET cc_start: 0.7346 (ttm) cc_final: 0.7089 (mtp) REVERT: A 1137 ASN cc_start: 0.8167 (m-40) cc_final: 0.7817 (m110) REVERT: A 1220 ILE cc_start: 0.7293 (OUTLIER) cc_final: 0.7073 (tp) outliers start: 43 outliers final: 26 residues processed: 148 average time/residue: 0.1602 time to fit residues: 37.4001 Evaluate side-chains 129 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN A1239 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9876 Z= 0.245 Angle : 0.731 10.156 13454 Z= 0.355 Chirality : 0.046 0.295 1573 Planarity : 0.004 0.041 1690 Dihedral : 8.684 64.770 1748 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.73 % Favored : 93.01 % Rotamer: Outliers : 4.15 % Allowed : 18.07 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.24), residues: 1188 helix: 0.92 (0.21), residues: 632 sheet: -1.01 (0.57), residues: 81 loop : -2.00 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 833 HIS 0.007 0.001 HIS A1042 PHE 0.028 0.002 PHE A 101 TYR 0.023 0.001 TYR A 677 ARG 0.005 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6446 (OUTLIER) cc_final: 0.5574 (t80) REVERT: A 436 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6683 (m-30) REVERT: A 622 PHE cc_start: 0.6317 (t80) cc_final: 0.5700 (m-10) REVERT: A 632 PHE cc_start: 0.7016 (t80) cc_final: 0.6546 (t80) REVERT: A 661 ILE cc_start: 0.7702 (mm) cc_final: 0.7428 (mm) REVERT: A 872 MET cc_start: 0.8017 (mmm) cc_final: 0.7580 (mmt) REVERT: A 1114 MET cc_start: 0.6882 (tmm) cc_final: 0.6262 (tmm) REVERT: A 1133 MET cc_start: 0.7355 (ttm) cc_final: 0.7067 (mtp) REVERT: A 1137 ASN cc_start: 0.8162 (m-40) cc_final: 0.7791 (m110) REVERT: A 1159 MET cc_start: 0.7894 (ttp) cc_final: 0.7599 (ttp) REVERT: A 1220 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.7102 (tp) outliers start: 43 outliers final: 32 residues processed: 139 average time/residue: 0.1747 time to fit residues: 38.2945 Evaluate side-chains 132 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9876 Z= 0.192 Angle : 0.689 10.376 13454 Z= 0.331 Chirality : 0.044 0.283 1573 Planarity : 0.004 0.041 1690 Dihedral : 8.198 61.797 1748 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.48 % Favored : 93.27 % Rotamer: Outliers : 3.57 % Allowed : 18.94 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.25), residues: 1188 helix: 1.08 (0.21), residues: 626 sheet: -0.83 (0.58), residues: 81 loop : -1.84 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 833 HIS 0.006 0.001 HIS A1042 PHE 0.023 0.001 PHE A 101 TYR 0.026 0.001 TYR A 677 ARG 0.005 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6423 (OUTLIER) cc_final: 0.5505 (t80) REVERT: A 436 ASP cc_start: 0.6902 (OUTLIER) cc_final: 0.6651 (m-30) REVERT: A 622 PHE cc_start: 0.6348 (t80) cc_final: 0.5753 (m-10) REVERT: A 632 PHE cc_start: 0.7021 (t80) cc_final: 0.6689 (t80) REVERT: A 872 MET cc_start: 0.7904 (mmm) cc_final: 0.7530 (mmm) REVERT: A 1089 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7022 (tm-30) REVERT: A 1114 MET cc_start: 0.6902 (tmm) cc_final: 0.6264 (tmm) REVERT: A 1133 MET cc_start: 0.7283 (ttm) cc_final: 0.6998 (mtp) REVERT: A 1137 ASN cc_start: 0.8137 (m-40) cc_final: 0.7764 (m110) outliers start: 37 outliers final: 28 residues processed: 130 average time/residue: 0.1609 time to fit residues: 32.8068 Evaluate side-chains 124 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1158 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 775 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9876 Z= 0.229 Angle : 0.706 10.204 13454 Z= 0.338 Chirality : 0.045 0.278 1573 Planarity : 0.004 0.041 1690 Dihedral : 7.963 58.674 1748 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.82 % Favored : 92.93 % Rotamer: Outliers : 4.25 % Allowed : 19.32 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.25), residues: 1188 helix: 1.02 (0.21), residues: 633 sheet: -0.76 (0.59), residues: 81 loop : -1.86 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 833 HIS 0.006 0.001 HIS A1042 PHE 0.028 0.002 PHE A 736 TYR 0.024 0.001 TYR A 677 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 91 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6490 (OUTLIER) cc_final: 0.5506 (t80) REVERT: A 436 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6719 (m-30) REVERT: A 622 PHE cc_start: 0.6452 (t80) cc_final: 0.5714 (m-10) REVERT: A 631 MET cc_start: 0.7503 (tmm) cc_final: 0.7302 (tmm) REVERT: A 1114 MET cc_start: 0.6883 (tmm) cc_final: 0.6212 (tmm) REVERT: A 1133 MET cc_start: 0.7355 (ttm) cc_final: 0.7086 (mtp) REVERT: A 1137 ASN cc_start: 0.8155 (m-40) cc_final: 0.7769 (m110) outliers start: 44 outliers final: 35 residues processed: 129 average time/residue: 0.1696 time to fit residues: 34.7981 Evaluate side-chains 128 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1239 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 90 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 556 ASN A1101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9876 Z= 0.190 Angle : 0.688 10.692 13454 Z= 0.329 Chirality : 0.044 0.269 1573 Planarity : 0.004 0.041 1690 Dihedral : 7.807 56.708 1748 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.69 % Rotamer: Outliers : 3.38 % Allowed : 20.19 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.25), residues: 1188 helix: 1.12 (0.21), residues: 633 sheet: -0.65 (0.60), residues: 81 loop : -1.76 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 833 HIS 0.006 0.001 HIS A1042 PHE 0.018 0.001 PHE A 769 TYR 0.014 0.001 TYR A1037 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.5783 (pttm) cc_final: 0.5154 (ttmm) REVERT: A 288 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.5594 (t80) REVERT: A 436 ASP cc_start: 0.6910 (OUTLIER) cc_final: 0.6581 (m-30) REVERT: A 622 PHE cc_start: 0.6479 (t80) cc_final: 0.5721 (m-10) REVERT: A 631 MET cc_start: 0.7388 (tmm) cc_final: 0.7186 (tmm) REVERT: A 872 MET cc_start: 0.7746 (mmm) cc_final: 0.7261 (mmm) REVERT: A 1114 MET cc_start: 0.6852 (tmm) cc_final: 0.6179 (tmm) REVERT: A 1133 MET cc_start: 0.7299 (ttm) cc_final: 0.7012 (mtp) REVERT: A 1137 ASN cc_start: 0.8121 (m-40) cc_final: 0.7753 (m110) outliers start: 35 outliers final: 30 residues processed: 130 average time/residue: 0.1692 time to fit residues: 34.4505 Evaluate side-chains 123 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1239 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9876 Z= 0.183 Angle : 0.683 10.552 13454 Z= 0.327 Chirality : 0.044 0.265 1573 Planarity : 0.004 0.041 1690 Dihedral : 7.597 55.269 1746 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.89 % Favored : 93.86 % Rotamer: Outliers : 3.48 % Allowed : 20.58 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.25), residues: 1188 helix: 1.22 (0.21), residues: 630 sheet: -0.60 (0.60), residues: 81 loop : -1.73 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 833 HIS 0.008 0.001 HIS A1042 PHE 0.017 0.001 PHE A 769 TYR 0.015 0.001 TYR A 555 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.5834 (pttm) cc_final: 0.5359 (tttp) REVERT: A 288 PHE cc_start: 0.6571 (OUTLIER) cc_final: 0.5519 (t80) REVERT: A 436 ASP cc_start: 0.6919 (OUTLIER) cc_final: 0.6590 (m-30) REVERT: A 622 PHE cc_start: 0.6489 (t80) cc_final: 0.5724 (m-10) REVERT: A 631 MET cc_start: 0.7490 (tmm) cc_final: 0.7262 (tmm) REVERT: A 1114 MET cc_start: 0.6845 (tmm) cc_final: 0.6171 (tmm) outliers start: 36 outliers final: 32 residues processed: 129 average time/residue: 0.1632 time to fit residues: 33.1182 Evaluate side-chains 128 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1239 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 94 optimal weight: 0.3980 chunk 9 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9876 Z= 0.176 Angle : 0.679 10.545 13454 Z= 0.325 Chirality : 0.044 0.265 1573 Planarity : 0.004 0.041 1690 Dihedral : 7.470 55.303 1746 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.89 % Favored : 93.86 % Rotamer: Outliers : 3.48 % Allowed : 20.68 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.25), residues: 1188 helix: 1.28 (0.21), residues: 630 sheet: -0.61 (0.60), residues: 81 loop : -1.69 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 833 HIS 0.008 0.001 HIS A1042 PHE 0.023 0.001 PHE A 632 TYR 0.013 0.001 TYR A1037 ARG 0.004 0.000 ARG A 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.5859 (pttm) cc_final: 0.5396 (tttp) REVERT: A 288 PHE cc_start: 0.6562 (OUTLIER) cc_final: 0.5524 (t80) REVERT: A 436 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6556 (m-30) REVERT: A 622 PHE cc_start: 0.6484 (t80) cc_final: 0.5728 (m-10) REVERT: A 631 MET cc_start: 0.7487 (tmm) cc_final: 0.7254 (tmm) REVERT: A 1114 MET cc_start: 0.6829 (tmm) cc_final: 0.6157 (tmm) outliers start: 36 outliers final: 32 residues processed: 137 average time/residue: 0.1657 time to fit residues: 35.8248 Evaluate side-chains 134 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1239 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.167070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.127827 restraints weight = 13744.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.126646 restraints weight = 8714.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.128135 restraints weight = 8220.779| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9876 Z= 0.204 Angle : 0.683 10.500 13454 Z= 0.327 Chirality : 0.044 0.269 1573 Planarity : 0.004 0.041 1690 Dihedral : 7.411 55.460 1746 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.57 % Favored : 93.18 % Rotamer: Outliers : 3.48 % Allowed : 20.39 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.25), residues: 1188 helix: 1.31 (0.21), residues: 630 sheet: -0.62 (0.60), residues: 81 loop : -1.73 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 260 HIS 0.008 0.001 HIS A1042 PHE 0.017 0.001 PHE A 769 TYR 0.015 0.001 TYR A1037 ARG 0.004 0.000 ARG A 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1804.80 seconds wall clock time: 34 minutes 5.21 seconds (2045.21 seconds total)