Starting phenix.real_space_refine on Wed Mar 4 18:15:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w5r_21545/03_2026/6w5r_21545.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5r_21545/03_2026/6w5r_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_21545/03_2026/6w5r_21545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5r_21545/03_2026/6w5r_21545.map" model { file = "/net/cci-nas-00/data/ceres_data/6w5r_21545/03_2026/6w5r_21545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5r_21545/03_2026/6w5r_21545.cif" } resolution = 3.6 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 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): 0.01s 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: 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: 2.15, per 1000 atoms: 0.22 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: 0.95 Conformation dependent library (CDL) restraints added in 474.0 milliseconds 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: 0.20 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: 1.24 Time building geometry restraints manager: 1.15 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.390 Find NCS groups from input model: 0.060 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.540 ------------------------------------------------------------------------------- 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 9910 Z= 0.723 Angle : 2.244 38.700 13541 Z= 1.228 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 : 4.94 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.82 % 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 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: -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 ARG 0.019 0.002 ARG A 789 TYR 0.046 0.007 TYR A 157 PHE 0.054 0.007 PHE A 108 TRP 0.038 0.005 TRP A 833 HIS 0.026 0.005 HIS A1042 Details of bonding type rmsd covalent geometry : bond 0.01518 ( 9876) covalent geometry : angle 2.10220 (13454) SS BOND : bond 0.01689 ( 15) SS BOND : angle 4.97081 ( 30) hydrogen bonds : bond 0.16096 ( 474) hydrogen bonds : angle 7.41009 ( 1374) link_ALPHA1-4 : bond 0.00153 ( 1) link_ALPHA1-4 : angle 0.18739 ( 3) link_BETA1-3 : bond 0.06299 ( 1) link_BETA1-3 : angle 28.87144 ( 3) link_BETA1-4 : bond 0.05450 ( 4) link_BETA1-4 : angle 18.24978 ( 12) link_NAG-ASN : bond 0.01394 ( 13) link_NAG-ASN : angle 6.20366 ( 39) *********************** 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 : 0.341 Fit side-chains REVERT: A 220 MET cc_start: 0.2696 (ppp) cc_final: 0.2255 (ptm) REVERT: A 272 MET cc_start: 0.6926 (mmp) cc_final: 0.6706 (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: 0.8509 (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: 0.0815 time to fit residues: 22.0436 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 : 0.338 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.169530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.132427 restraints weight = 14872.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130415 restraints weight = 8820.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.132025 restraints weight = 8273.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132485 restraints weight = 5585.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132881 restraints weight = 5231.748| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9910 Z= 0.164 Angle : 0.894 12.505 13541 Z= 0.422 Chirality : 0.050 0.376 1573 Planarity : 0.005 0.045 1690 Dihedral : 13.364 93.573 1769 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.23 % Favored : 93.52 % 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 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: -1.66 (0.23), residues: 1188 helix: 0.02 (0.20), residues: 625 sheet: -1.33 (0.69), residues: 59 loop : -2.56 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 39 TYR 0.016 0.002 TYR A 146 PHE 0.023 0.002 PHE A 101 TRP 0.019 0.002 TRP A 291 HIS 0.009 0.001 HIS A1029 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9876) covalent geometry : angle 0.85189 (13454) SS BOND : bond 0.00500 ( 15) SS BOND : angle 1.93081 ( 30) hydrogen bonds : bond 0.05069 ( 474) hydrogen bonds : angle 5.07021 ( 1374) link_ALPHA1-4 : bond 0.00497 ( 1) link_ALPHA1-4 : angle 3.19981 ( 3) link_BETA1-3 : bond 0.01771 ( 1) link_BETA1-3 : angle 7.39775 ( 3) link_BETA1-4 : bond 0.00522 ( 4) link_BETA1-4 : angle 4.28881 ( 12) link_NAG-ASN : bond 0.00535 ( 13) link_NAG-ASN : angle 3.68672 ( 39) *********************** 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 150 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.361 Fit side-chains REVERT: A 145 GLN cc_start: 0.4800 (OUTLIER) cc_final: 0.4574 (pp30) REVERT: A 220 MET cc_start: 0.2133 (ppp) cc_final: 0.1358 (ptm) REVERT: A 436 ASP cc_start: 0.6757 (OUTLIER) cc_final: 0.6504 (m-30) REVERT: A 622 PHE cc_start: 0.6538 (t80) cc_final: 0.5800 (m-10) REVERT: A 724 LEU cc_start: 0.8205 (tp) cc_final: 0.7939 (tp) REVERT: A 769 PHE cc_start: 0.8701 (t80) cc_final: 0.8417 (t80) REVERT: A 1133 MET cc_start: 0.7395 (ttm) cc_final: 0.7187 (mtp) REVERT: A 1137 ASN cc_start: 0.8086 (m-40) cc_final: 0.7852 (m110) REVERT: A 1197 SER cc_start: 0.8764 (m) cc_final: 0.8526 (t) outliers start: 33 outliers final: 15 residues processed: 145 average time/residue: 0.0672 time to fit residues: 15.2436 Evaluate side-chains 118 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 31 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 581 GLN A 596 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.170422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.132694 restraints weight = 13671.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130707 restraints weight = 8525.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132728 restraints weight = 8078.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133122 restraints weight = 5129.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133673 restraints weight = 4744.401| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9910 Z= 0.145 Angle : 0.811 11.377 13541 Z= 0.380 Chirality : 0.048 0.300 1573 Planarity : 0.004 0.042 1690 Dihedral : 10.901 82.812 1752 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.65 % Favored : 93.10 % Rotamer: Outliers : 3.29 % Allowed : 15.56 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.97 (0.24), residues: 1188 helix: 0.68 (0.21), residues: 625 sheet: -1.50 (0.59), residues: 71 loop : -2.31 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.012 0.001 TYR A 457 PHE 0.022 0.001 PHE A 101 TRP 0.023 0.001 TRP A 291 HIS 0.007 0.001 HIS A1029 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9876) covalent geometry : angle 0.77413 (13454) SS BOND : bond 0.00575 ( 15) SS BOND : angle 1.63942 ( 30) hydrogen bonds : bond 0.04303 ( 474) hydrogen bonds : angle 4.76301 ( 1374) link_ALPHA1-4 : bond 0.00191 ( 1) link_ALPHA1-4 : angle 3.14309 ( 3) link_BETA1-3 : bond 0.01317 ( 1) link_BETA1-3 : angle 6.41667 ( 3) link_BETA1-4 : bond 0.01071 ( 4) link_BETA1-4 : angle 3.61939 ( 12) link_NAG-ASN : bond 0.00609 ( 13) link_NAG-ASN : angle 3.38062 ( 39) *********************** 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 149 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 220 MET cc_start: 0.2522 (ppp) cc_final: 0.1588 (ptm) REVERT: A 288 PHE cc_start: 0.6511 (OUTLIER) cc_final: 0.5797 (t80) REVERT: A 436 ASP cc_start: 0.6676 (OUTLIER) cc_final: 0.6387 (m-30) REVERT: A 551 ASP cc_start: 0.8345 (p0) cc_final: 0.8106 (p0) REVERT: A 622 PHE cc_start: 0.6378 (t80) cc_final: 0.5653 (m-10) REVERT: A 700 ASP cc_start: 0.7863 (t0) cc_final: 0.7596 (t0) REVERT: A 858 ILE cc_start: 0.9063 (mm) cc_final: 0.8818 (mt) REVERT: A 1133 MET cc_start: 0.7383 (ttm) cc_final: 0.7149 (mtp) REVERT: A 1137 ASN cc_start: 0.8227 (m-40) cc_final: 0.7965 (m110) REVERT: A 1159 MET cc_start: 0.8087 (ttm) cc_final: 0.7844 (ttp) REVERT: A 1197 SER cc_start: 0.8812 (m) cc_final: 0.8513 (p) REVERT: A 1220 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7197 (tp) outliers start: 34 outliers final: 19 residues processed: 142 average time/residue: 0.0623 time to fit residues: 14.1839 Evaluate side-chains 125 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 483 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 731 VAL 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 909 CYS Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1043 THR 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 39 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 84 optimal weight: 0.0270 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.168066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.129583 restraints weight = 13751.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129286 restraints weight = 8075.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.130111 restraints weight = 8697.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.131048 restraints weight = 5320.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.131438 restraints weight = 4622.073| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9910 Z= 0.153 Angle : 0.769 10.623 13541 Z= 0.360 Chirality : 0.046 0.297 1573 Planarity : 0.004 0.052 1690 Dihedral : 9.421 67.879 1748 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.73 % Favored : 93.01 % Rotamer: Outliers : 4.35 % Allowed : 16.43 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.60 (0.24), residues: 1188 helix: 0.88 (0.21), residues: 632 sheet: -1.19 (0.62), residues: 71 loop : -2.06 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.014 0.001 TYR A1037 PHE 0.028 0.002 PHE A 769 TRP 0.015 0.001 TRP A 291 HIS 0.007 0.001 HIS A1042 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9876) covalent geometry : angle 0.73568 (13454) SS BOND : bond 0.00522 ( 15) SS BOND : angle 1.65191 ( 30) hydrogen bonds : bond 0.04140 ( 474) hydrogen bonds : angle 4.73973 ( 1374) link_ALPHA1-4 : bond 0.00051 ( 1) link_ALPHA1-4 : angle 3.04638 ( 3) link_BETA1-3 : bond 0.01035 ( 1) link_BETA1-3 : angle 5.51859 ( 3) link_BETA1-4 : bond 0.01047 ( 4) link_BETA1-4 : angle 3.34639 ( 12) link_NAG-ASN : bond 0.00435 ( 13) link_NAG-ASN : angle 3.13603 ( 39) *********************** 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 154 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 109 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6391 (OUTLIER) cc_final: 0.5620 (t80) REVERT: A 436 ASP cc_start: 0.6776 (OUTLIER) cc_final: 0.6483 (m-30) REVERT: A 622 PHE cc_start: 0.6396 (t80) cc_final: 0.5610 (m-10) REVERT: A 661 ILE cc_start: 0.7819 (mm) cc_final: 0.7546 (mm) REVERT: A 858 ILE cc_start: 0.9151 (mm) cc_final: 0.8945 (mt) REVERT: A 872 MET cc_start: 0.7945 (mmm) cc_final: 0.7604 (mmm) REVERT: A 1133 MET cc_start: 0.7496 (ttm) cc_final: 0.7239 (mtp) REVERT: A 1137 ASN cc_start: 0.8153 (m-40) cc_final: 0.7821 (m110) REVERT: A 1159 MET cc_start: 0.8143 (ttm) cc_final: 0.7935 (ttp) REVERT: A 1220 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7195 (tp) outliers start: 45 outliers final: 28 residues processed: 147 average time/residue: 0.0642 time to fit residues: 15.1490 Evaluate side-chains 131 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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 574 THR 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 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 99 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 45 optimal weight: 0.0470 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.171790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.133376 restraints weight = 13665.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.133829 restraints weight = 8152.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.135395 restraints weight = 7437.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135835 restraints weight = 4731.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136488 restraints weight = 4456.024| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9910 Z= 0.130 Angle : 0.728 10.318 13541 Z= 0.342 Chirality : 0.045 0.281 1573 Planarity : 0.004 0.042 1690 Dihedral : 8.572 64.347 1748 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.47 % Favored : 94.28 % Rotamer: Outliers : 3.48 % Allowed : 18.36 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.27 (0.25), residues: 1188 helix: 1.13 (0.21), residues: 621 sheet: -0.79 (0.57), residues: 81 loop : -1.86 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.010 0.001 TYR A1037 PHE 0.028 0.001 PHE A 101 TRP 0.012 0.001 TRP A 291 HIS 0.007 0.001 HIS A1042 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9876) covalent geometry : angle 0.69676 (13454) SS BOND : bond 0.00436 ( 15) SS BOND : angle 1.86103 ( 30) hydrogen bonds : bond 0.03915 ( 474) hydrogen bonds : angle 4.63971 ( 1374) link_ALPHA1-4 : bond 0.00266 ( 1) link_ALPHA1-4 : angle 3.18619 ( 3) link_BETA1-3 : bond 0.00674 ( 1) link_BETA1-3 : angle 5.39433 ( 3) link_BETA1-4 : bond 0.01081 ( 4) link_BETA1-4 : angle 3.24769 ( 12) link_NAG-ASN : bond 0.00493 ( 13) link_NAG-ASN : angle 2.72209 ( 39) *********************** 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 143 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6482 (OUTLIER) cc_final: 0.5563 (t80) REVERT: A 436 ASP cc_start: 0.6808 (OUTLIER) cc_final: 0.6454 (m-30) REVERT: A 496 ASP cc_start: 0.7312 (m-30) cc_final: 0.7111 (m-30) REVERT: A 622 PHE cc_start: 0.6488 (t80) cc_final: 0.5790 (m-10) REVERT: A 661 ILE cc_start: 0.7812 (mm) cc_final: 0.7584 (mm) REVERT: A 858 ILE cc_start: 0.9088 (mm) cc_final: 0.8885 (mt) REVERT: A 872 MET cc_start: 0.7899 (mmm) cc_final: 0.7450 (mmt) REVERT: A 1114 MET cc_start: 0.6814 (tmm) cc_final: 0.6565 (tmm) REVERT: A 1133 MET cc_start: 0.7387 (ttm) cc_final: 0.7119 (mtp) REVERT: A 1137 ASN cc_start: 0.8189 (m-40) cc_final: 0.7871 (m110) REVERT: A 1159 MET cc_start: 0.8092 (ttm) cc_final: 0.7851 (ttp) outliers start: 36 outliers final: 23 residues processed: 140 average time/residue: 0.0653 time to fit residues: 14.6389 Evaluate side-chains 121 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 162 ASP 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 452 ASN 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 817 LEU 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 1036 THR Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1158 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 84 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.171236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.133352 restraints weight = 13724.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132967 restraints weight = 8284.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.134314 restraints weight = 8007.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134841 restraints weight = 5069.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.135218 restraints weight = 4596.120| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9910 Z= 0.130 Angle : 0.721 10.377 13541 Z= 0.337 Chirality : 0.045 0.360 1573 Planarity : 0.004 0.040 1690 Dihedral : 8.108 61.491 1748 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.98 % Favored : 93.77 % Rotamer: Outliers : 3.67 % Allowed : 18.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.25), residues: 1188 helix: 1.20 (0.21), residues: 624 sheet: -0.70 (0.58), residues: 81 loop : -1.75 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.028 0.001 TYR A 677 PHE 0.026 0.001 PHE A 101 TRP 0.009 0.001 TRP A 833 HIS 0.009 0.001 HIS A1042 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9876) covalent geometry : angle 0.68430 (13454) SS BOND : bond 0.00467 ( 15) SS BOND : angle 1.73412 ( 30) hydrogen bonds : bond 0.03754 ( 474) hydrogen bonds : angle 4.57976 ( 1374) link_ALPHA1-4 : bond 0.00013 ( 1) link_ALPHA1-4 : angle 3.24071 ( 3) link_BETA1-3 : bond 0.00539 ( 1) link_BETA1-3 : angle 5.10968 ( 3) link_BETA1-4 : bond 0.01074 ( 4) link_BETA1-4 : angle 3.28361 ( 12) link_NAG-ASN : bond 0.00581 ( 13) link_NAG-ASN : angle 3.23625 ( 39) *********************** 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 141 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.6819 (mp) cc_final: 0.6497 (tt) REVERT: A 288 PHE cc_start: 0.6461 (OUTLIER) cc_final: 0.5548 (t80) REVERT: A 436 ASP cc_start: 0.6814 (m-30) cc_final: 0.6475 (m-30) REVERT: A 551 ASP cc_start: 0.8333 (p0) cc_final: 0.8095 (p0) REVERT: A 622 PHE cc_start: 0.6334 (t80) cc_final: 0.5757 (m-10) REVERT: A 1114 MET cc_start: 0.6830 (tmm) cc_final: 0.6521 (tmm) REVERT: A 1133 MET cc_start: 0.7441 (ttm) cc_final: 0.7175 (mtp) REVERT: A 1137 ASN cc_start: 0.8209 (m-40) cc_final: 0.7906 (m110) REVERT: A 1159 MET cc_start: 0.8079 (ttm) cc_final: 0.7788 (ttp) outliers start: 38 outliers final: 30 residues processed: 138 average time/residue: 0.0661 time to fit residues: 14.5293 Evaluate side-chains 128 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 126 THR 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 452 ASN Chi-restraints excluded: chain A residue 556 ASN 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 A 925 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.172257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.134301 restraints weight = 13678.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.133985 restraints weight = 8907.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135413 restraints weight = 8296.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.135997 restraints weight = 5176.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136431 restraints weight = 4713.447| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9910 Z= 0.133 Angle : 0.722 10.094 13541 Z= 0.337 Chirality : 0.044 0.270 1573 Planarity : 0.004 0.041 1690 Dihedral : 7.733 58.277 1746 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.72 % Favored : 94.02 % Rotamer: Outliers : 3.86 % Allowed : 18.65 % 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 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: -0.12 (0.25), residues: 1188 helix: 1.19 (0.21), residues: 631 sheet: -0.69 (0.60), residues: 81 loop : -1.75 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.023 0.001 TYR A 677 PHE 0.027 0.001 PHE A 736 TRP 0.014 0.001 TRP A 189 HIS 0.008 0.001 HIS A1042 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9876) covalent geometry : angle 0.69095 (13454) SS BOND : bond 0.00288 ( 15) SS BOND : angle 1.89849 ( 30) hydrogen bonds : bond 0.03747 ( 474) hydrogen bonds : angle 4.58707 ( 1374) link_ALPHA1-4 : bond 0.00105 ( 1) link_ALPHA1-4 : angle 3.30494 ( 3) link_BETA1-3 : bond 0.00617 ( 1) link_BETA1-3 : angle 4.86014 ( 3) link_BETA1-4 : bond 0.01092 ( 4) link_BETA1-4 : angle 3.34006 ( 12) link_NAG-ASN : bond 0.00382 ( 13) link_NAG-ASN : angle 2.69439 ( 39) *********************** 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 142 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 102 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.6121 (pttm) cc_final: 0.5850 (pptt) REVERT: A 288 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.5531 (t80) REVERT: A 436 ASP cc_start: 0.6851 (m-30) cc_final: 0.6497 (m-30) REVERT: A 622 PHE cc_start: 0.6311 (t80) cc_final: 0.5757 (m-10) REVERT: A 1114 MET cc_start: 0.6776 (tmm) cc_final: 0.6441 (tmm) outliers start: 40 outliers final: 34 residues processed: 139 average time/residue: 0.0644 time to fit residues: 14.4045 Evaluate side-chains 129 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 126 THR Chi-restraints excluded: chain A residue 133 VAL 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 408 LEU Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 556 ASN 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 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 1158 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 44 optimal weight: 0.0370 chunk 39 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 0.0070 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 A1239 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.172108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.134083 restraints weight = 13821.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.132968 restraints weight = 9068.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.134786 restraints weight = 7701.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.135355 restraints weight = 5019.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135718 restraints weight = 4927.039| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9910 Z= 0.119 Angle : 0.709 10.532 13541 Z= 0.331 Chirality : 0.045 0.389 1573 Planarity : 0.004 0.041 1690 Dihedral : 7.581 55.916 1746 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.64 % Favored : 94.11 % Rotamer: Outliers : 3.57 % Allowed : 19.61 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.01 (0.25), residues: 1188 helix: 1.26 (0.21), residues: 631 sheet: -0.52 (0.60), residues: 81 loop : -1.67 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.014 0.001 TYR A 677 PHE 0.022 0.001 PHE A 632 TRP 0.007 0.001 TRP A 291 HIS 0.007 0.001 HIS A1042 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9876) covalent geometry : angle 0.68249 (13454) SS BOND : bond 0.00420 ( 15) SS BOND : angle 1.56052 ( 30) hydrogen bonds : bond 0.03588 ( 474) hydrogen bonds : angle 4.56375 ( 1374) link_ALPHA1-4 : bond 0.00036 ( 1) link_ALPHA1-4 : angle 3.29616 ( 3) link_BETA1-3 : bond 0.00627 ( 1) link_BETA1-3 : angle 4.63184 ( 3) link_BETA1-4 : bond 0.01028 ( 4) link_BETA1-4 : angle 3.30329 ( 12) link_NAG-ASN : bond 0.00387 ( 13) link_NAG-ASN : angle 2.42650 ( 39) *********************** 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 140 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.6003 (pttm) cc_final: 0.5549 (ttmm) REVERT: A 288 PHE cc_start: 0.6492 (OUTLIER) cc_final: 0.5392 (t80) REVERT: A 436 ASP cc_start: 0.6773 (m-30) cc_final: 0.6438 (m-30) REVERT: A 1114 MET cc_start: 0.6733 (tmm) cc_final: 0.6369 (tmm) REVERT: A 1159 MET cc_start: 0.8037 (ttp) cc_final: 0.7802 (ttp) outliers start: 37 outliers final: 31 residues processed: 137 average time/residue: 0.0655 time to fit residues: 14.5139 Evaluate side-chains 131 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 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 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 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 91 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN A1101 ASN A1239 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.169679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.130563 restraints weight = 13608.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.130768 restraints weight = 8512.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.131998 restraints weight = 8010.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.132501 restraints weight = 5594.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133040 restraints weight = 5129.644| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9910 Z= 0.128 Angle : 0.711 10.735 13541 Z= 0.332 Chirality : 0.045 0.351 1573 Planarity : 0.004 0.041 1690 Dihedral : 7.428 55.366 1746 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.56 % Favored : 94.19 % 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 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: 0.07 (0.25), residues: 1188 helix: 1.29 (0.21), residues: 637 sheet: -0.51 (0.60), residues: 81 loop : -1.63 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.013 0.001 TYR A1037 PHE 0.017 0.001 PHE A 769 TRP 0.008 0.001 TRP A 833 HIS 0.011 0.001 HIS A1239 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9876) covalent geometry : angle 0.68606 (13454) SS BOND : bond 0.00375 ( 15) SS BOND : angle 1.64936 ( 30) hydrogen bonds : bond 0.03655 ( 474) hydrogen bonds : angle 4.56571 ( 1374) link_ALPHA1-4 : bond 0.00171 ( 1) link_ALPHA1-4 : angle 3.39862 ( 3) link_BETA1-3 : bond 0.00505 ( 1) link_BETA1-3 : angle 4.47602 ( 3) link_BETA1-4 : bond 0.01053 ( 4) link_BETA1-4 : angle 3.40655 ( 12) link_NAG-ASN : bond 0.00356 ( 13) link_NAG-ASN : angle 2.24787 ( 39) *********************** 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 132 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.5867 (pttm) cc_final: 0.5596 (tttp) REVERT: A 436 ASP cc_start: 0.6810 (m-30) cc_final: 0.6462 (m-30) REVERT: A 496 ASP cc_start: 0.7445 (m-30) cc_final: 0.7233 (m-30) REVERT: A 622 PHE cc_start: 0.6484 (t80) cc_final: 0.5748 (m-10) REVERT: A 1114 MET cc_start: 0.6727 (tmm) cc_final: 0.6311 (tmm) outliers start: 35 outliers final: 33 residues processed: 129 average time/residue: 0.0642 time to fit residues: 13.1765 Evaluate side-chains 127 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 292 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 408 LEU 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 861 ASP Chi-restraints excluded: chain A residue 879 ILE 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 15 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 63 optimal weight: 0.0980 chunk 113 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 12 optimal weight: 0.0000 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.170257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.131605 restraints weight = 13606.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.131412 restraints weight = 8399.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133157 restraints weight = 7723.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.133545 restraints weight = 4892.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.134031 restraints weight = 4534.398| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9910 Z= 0.120 Angle : 0.696 10.614 13541 Z= 0.326 Chirality : 0.044 0.321 1573 Planarity : 0.004 0.041 1690 Dihedral : 7.338 55.396 1746 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.72 % Favored : 94.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.25), residues: 1188 helix: 1.34 (0.21), residues: 636 sheet: -0.43 (0.61), residues: 81 loop : -1.60 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.021 0.001 TYR A 677 PHE 0.023 0.001 PHE A 632 TRP 0.007 0.001 TRP A 833 HIS 0.009 0.001 HIS A1042 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9876) covalent geometry : angle 0.67186 (13454) SS BOND : bond 0.00348 ( 15) SS BOND : angle 1.57075 ( 30) hydrogen bonds : bond 0.03592 ( 474) hydrogen bonds : angle 4.53990 ( 1374) link_ALPHA1-4 : bond 0.00201 ( 1) link_ALPHA1-4 : angle 3.38669 ( 3) link_BETA1-3 : bond 0.00506 ( 1) link_BETA1-3 : angle 4.37874 ( 3) link_BETA1-4 : bond 0.01057 ( 4) link_BETA1-4 : angle 3.41654 ( 12) link_NAG-ASN : bond 0.00364 ( 13) link_NAG-ASN : angle 2.15596 ( 39) ********************** 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 133 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.5920 (pttm) cc_final: 0.5656 (tttp) REVERT: A 288 PHE cc_start: 0.6485 (OUTLIER) cc_final: 0.5443 (t80) REVERT: A 436 ASP cc_start: 0.6817 (m-30) cc_final: 0.6448 (m-30) REVERT: A 1114 MET cc_start: 0.6746 (tmm) cc_final: 0.6278 (tmm) outliers start: 35 outliers final: 31 residues processed: 130 average time/residue: 0.0637 time to fit residues: 13.2944 Evaluate side-chains 127 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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 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 861 ASP Chi-restraints excluded: chain A residue 879 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 18 optimal weight: 40.0000 chunk 86 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.170092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.131455 restraints weight = 13740.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.131717 restraints weight = 8645.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133054 restraints weight = 7658.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.133797 restraints weight = 4843.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134264 restraints weight = 4486.797| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9910 Z= 0.123 Angle : 0.698 11.659 13541 Z= 0.325 Chirality : 0.044 0.287 1573 Planarity : 0.004 0.041 1690 Dihedral : 7.149 55.171 1746 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.81 % Favored : 94.02 % Rotamer: Outliers : 3.19 % Allowed : 20.87 % 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 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: 0.20 (0.25), residues: 1188 helix: 1.39 (0.21), residues: 635 sheet: -0.40 (0.61), residues: 81 loop : -1.57 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.024 0.001 TYR A 102 PHE 0.017 0.001 PHE A 769 TRP 0.012 0.001 TRP A 189 HIS 0.008 0.001 HIS A1042 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9876) covalent geometry : angle 0.67495 (13454) SS BOND : bond 0.00356 ( 15) SS BOND : angle 1.60863 ( 30) hydrogen bonds : bond 0.03587 ( 474) hydrogen bonds : angle 4.52233 ( 1374) link_ALPHA1-4 : bond 0.00065 ( 1) link_ALPHA1-4 : angle 3.42036 ( 3) link_BETA1-3 : bond 0.00528 ( 1) link_BETA1-3 : angle 4.16318 ( 3) link_BETA1-4 : bond 0.01111 ( 4) link_BETA1-4 : angle 3.49626 ( 12) link_NAG-ASN : bond 0.00354 ( 13) link_NAG-ASN : angle 2.05972 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1463.25 seconds wall clock time: 25 minutes 59.04 seconds (1559.04 seconds total)