Starting phenix.real_space_refine on Sat Sep 12 11:01:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w5r_21545/09_2026/6w5r_21545.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5r_21545/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6w5r_21545/09_2026/6w5r_21545.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w5r_21545/09_2026/6w5r_21545.cif" model { file = "/net/cci-nas-00/data/ceres_data/6w5r_21545/09_2026/6w5r_21545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5r_21545/09_2026/6w5r_21545.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w5r_21545/09_2026/6w5r_21545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5r_21545/09_2026/6w5r_21545.map" } 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-2.2.1-6174/lib/python3.11/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 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 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 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 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 chiralities: 9 Time building chain proxies: 1.97, per 1000 atoms: 0.20 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: 0.67 Conformation dependent library (CDL) restraints added in 277.2 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: 0.29 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: 1.48 Time building geometry restraints manager: 0.96 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 - 17.68: 5078 17.68 - 35.35: 473 35.35 - 53.03: 106 53.03 - 70.70: 23 70.70 - 88.38: 4 Dihedral angle restraints: 5684 sinusoidal: 2204 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 5681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.954: 1570 0.954 - 1.909: 2 1.909 - 2.863: 0 2.863 - 3.818: 0 3.818 - 4.772: 1 Chirality restraints: 1573 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 2.37 -4.77 2.00e-02 2.50e+03 5.69e+04 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-02 2.50e+03 6.85e+03 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.01 -1.39 2.00e-02 2.50e+03 4.84e+03 ... (remaining 1570 not shown) Planarity restraints: 1703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.316 2.00e-02 2.50e+03 2.69e-01 9.04e+02 pdb=" C7 NAG E 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.182 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.468 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " -0.086 2.00e-02 2.50e+03 7.12e-02 6.33e+01 pdb=" C7 NAG C 2 " 0.024 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " -0.065 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " 0.113 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 107 " 0.035 2.00e-02 2.50e+03 6.97e-02 4.85e+01 pdb=" C LEU A 107 " -0.121 2.00e-02 2.50e+03 pdb=" O LEU A 107 " 0.045 2.00e-02 2.50e+03 pdb=" N PHE A 108 " 0.041 2.00e-02 2.50e+03 ... (remaining 1700 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 109 2.62 - 3.19: 7763 3.19 - 3.76: 14485 3.76 - 4.33: 18982 4.33 - 4.90: 32224 Nonbonded interactions: 73563 Sorted by model distance: nonbonded pdb=" O4 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.053 3.040 nonbonded pdb=" O ASP A 508 " pdb=" OG1 THR A 511 " model vdw 2.328 3.040 nonbonded pdb=" OG SER A 366 " pdb=" OH TYR A 677 " model vdw 2.341 3.040 nonbonded pdb=" O SER A 970 " pdb=" OG SER A 970 " model vdw 2.349 3.040 nonbonded pdb=" O ALA A1192 " pdb=" OG SER A1196 " model vdw 2.359 3.040 ... (remaining 73558 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'E' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.290 Find NCS groups from input model: 0.160 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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 : 14.242 88.376 3401 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/Z covalent geometry : bond 0.01518 / 0.72 ( 9876) covalent geometry : angle 2.10220 / 1.20 (13454) SS BOND : bond 0.01689 / 0.88 ( 15) SS BOND : angle 4.97081 / 3.05 ( 30) hydrogen bonds : bond 0.16096 / 10.62 ( 474) hydrogen bonds : angle 7.41009 / 5.07 ( 1374) link_ALPHA1-4 : bond 0.00153 / 0.08 ( 1) link_ALPHA1-4 : angle 0.18739 / 0.11 ( 3) link_BETA1-3 : bond 0.06299 / 3.32 ( 1) link_BETA1-3 : angle 28.87144 / 15.25 ( 3) link_BETA1-4 : bond 0.05450 / 2.73 ( 4) link_BETA1-4 : angle 18.24978 / 10.41 ( 12) link_NAG-ASN : bond 0.01394 / 0.77 ( 13) link_NAG-ASN : angle 6.20366 / 5.53 ( 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 : 0.336 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: 0.0747 time to fit residues: 20.0606 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 : 0.362 ------------------------------------------------------------------------------- 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... A 41 ASN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 145 GLN A 185 ASN A 442 GLN A 465 GLN A 476 ASN A 581 GLN A 701 ASN A 707 GLN A 897 HIS A 905 GLN A 906 ASN A1016 HIS ** A1029 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN A1193 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.169479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.132271 restraints weight = 14819.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.129832 restraints weight = 8362.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131674 restraints weight = 7968.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.132064 restraints weight = 5459.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.132378 restraints weight = 5004.431| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9910 Z= 0.164 Angle : 0.871 12.268 13541 Z= 0.416 Chirality : 0.051 0.356 1573 Planarity : 0.005 0.043 1690 Dihedral : 7.220 56.956 1318 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: -1.63 (0.23), residues: 1188 helix: 0.06 (0.20), residues: 623 sheet: -1.34 (0.69), residues: 59 loop : -2.56 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 78 TYR 0.015 0.002 TYR A 146 PHE 0.023 0.002 PHE A 101 TRP 0.020 0.002 TRP A 291 HIS 0.009 0.001 HIS A1029 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 9876) covalent geometry : angle 0.83269 / 0.41 (13454) SS BOND : bond 0.00350 / 0.24 ( 15) SS BOND : angle 1.98365 / 1.35 ( 30) hydrogen bonds : bond 0.05003 / 3.29 ( 474) hydrogen bonds : angle 5.04668 / 3.45 ( 1374) link_ALPHA1-4 : bond 0.00756 / 0.40 ( 1) link_ALPHA1-4 : angle 1.35289 / 0.77 ( 3) link_BETA1-3 : bond 0.01527 / 0.80 ( 1) link_BETA1-3 : angle 6.92859 / 3.68 ( 3) link_BETA1-4 : bond 0.00757 / 0.38 ( 4) link_BETA1-4 : angle 3.99446 / 2.28 ( 12) link_NAG-ASN : bond 0.00589 / 0.29 ( 13) link_NAG-ASN : angle 3.52820 / 3.06 ( 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 151 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.238 Fit side-chains REVERT: A 145 GLN cc_start: 0.4789 (OUTLIER) cc_final: 0.4551 (pp30) REVERT: A 220 MET cc_start: 0.2298 (ppp) cc_final: 0.1429 (ptm) REVERT: A 436 ASP cc_start: 0.6784 (OUTLIER) cc_final: 0.6527 (m-30) REVERT: A 622 PHE cc_start: 0.6471 (t80) cc_final: 0.5709 (m-10) REVERT: A 724 LEU cc_start: 0.8191 (tp) cc_final: 0.7907 (tp) REVERT: A 769 PHE cc_start: 0.8692 (t80) cc_final: 0.8407 (t80) REVERT: A 1114 MET cc_start: 0.7156 (tmm) cc_final: 0.6941 (tmm) REVERT: A 1133 MET cc_start: 0.7344 (ttm) cc_final: 0.7137 (mtp) REVERT: A 1137 ASN cc_start: 0.8060 (m-40) cc_final: 0.7826 (m110) REVERT: A 1197 SER cc_start: 0.8759 (m) cc_final: 0.8524 (t) outliers start: 33 outliers final: 15 residues processed: 146 average time/residue: 0.0601 time to fit residues: 13.6425 Evaluate side-chains 119 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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: 0.6980 chunk 110 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4143 r_free = 0.4143 target = 0.170698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.132503 restraints weight = 13663.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.132428 restraints weight = 7922.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.133213 restraints weight = 8700.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.134264 restraints weight = 5171.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.137553 restraints weight = 4428.851| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9910 Z= 0.143 Angle : 0.771 10.608 13541 Z= 0.371 Chirality : 0.048 0.331 1573 Planarity : 0.004 0.040 1690 Dihedral : 6.118 55.818 1301 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.65 % Favored : 93.10 % Rotamer: Outliers : 3.19 % Allowed : 15.65 % 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: -0.98 (0.24), residues: 1188 helix: 0.68 (0.21), residues: 625 sheet: -1.53 (0.58), residues: 71 loop : -2.33 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.013 0.001 TYR A 457 PHE 0.025 0.001 PHE A 101 TRP 0.014 0.001 TRP A 291 HIS 0.007 0.001 HIS A1029 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 9876) covalent geometry : angle 0.74083 / 0.36 (13454) SS BOND : bond 0.00701 / 0.38 ( 15) SS BOND : angle 1.72780 / 1.15 ( 30) hydrogen bonds : bond 0.04317 / 2.84 ( 474) hydrogen bonds : angle 4.75805 / 3.26 ( 1374) link_ALPHA1-4 : bond 0.00556 / 0.29 ( 1) link_ALPHA1-4 : angle 1.41483 / 0.76 ( 3) link_BETA1-3 : bond 0.01566 / 0.82 ( 1) link_BETA1-3 : angle 6.59302 / 3.55 ( 3) link_BETA1-4 : bond 0.01144 / 0.57 ( 4) link_BETA1-4 : angle 3.15156 / 1.81 ( 12) link_NAG-ASN : bond 0.00685 / 0.33 ( 13) link_NAG-ASN : angle 2.83712 / 2.48 ( 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 147 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 220 MET cc_start: 0.2539 (ppp) cc_final: 0.1637 (ptm) REVERT: A 288 PHE cc_start: 0.6595 (OUTLIER) cc_final: 0.5900 (t80) REVERT: A 436 ASP cc_start: 0.6661 (OUTLIER) cc_final: 0.6377 (m-30) REVERT: A 622 PHE cc_start: 0.6490 (t80) cc_final: 0.5794 (m-10) REVERT: A 700 ASP cc_start: 0.7779 (t0) cc_final: 0.7568 (t0) REVERT: A 858 ILE cc_start: 0.9041 (mm) cc_final: 0.8795 (mt) REVERT: A 1114 MET cc_start: 0.6952 (tmm) cc_final: 0.6563 (tmm) REVERT: A 1133 MET cc_start: 0.7425 (ttm) cc_final: 0.7214 (mtp) REVERT: A 1137 ASN cc_start: 0.8244 (m-40) cc_final: 0.7976 (m110) REVERT: A 1159 MET cc_start: 0.8102 (ttm) cc_final: 0.7853 (ttp) REVERT: A 1197 SER cc_start: 0.8776 (m) cc_final: 0.8476 (p) REVERT: A 1220 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7207 (tp) outliers start: 33 outliers final: 19 residues processed: 140 average time/residue: 0.0665 time to fit residues: 14.8670 Evaluate side-chains 124 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 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: 2.9990 chunk 90 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.167478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.128662 restraints weight = 13753.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128147 restraints weight = 7932.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128922 restraints weight = 9023.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.130044 restraints weight = 5554.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.133687 restraints weight = 4737.014| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9910 Z= 0.161 Angle : 0.761 10.598 13541 Z= 0.360 Chirality : 0.048 0.328 1573 Planarity : 0.004 0.055 1690 Dihedral : 5.815 55.523 1297 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.65 % Favored : 93.10 % Rotamer: Outliers : 4.54 % Allowed : 16.14 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.24), residues: 1188 helix: 0.88 (0.21), residues: 631 sheet: -1.24 (0.62), residues: 71 loop : -2.10 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.021 0.001 TYR A 677 PHE 0.027 0.002 PHE A 769 TRP 0.014 0.001 TRP A 833 HIS 0.007 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 9876) covalent geometry : angle 0.73399 / 0.35 (13454) SS BOND : bond 0.00426 / 0.21 ( 15) SS BOND : angle 1.56970 / 1.02 ( 30) hydrogen bonds : bond 0.04189 / 2.74 ( 474) hydrogen bonds : angle 4.76306 / 3.27 ( 1374) link_ALPHA1-4 : bond 0.00666 / 0.35 ( 1) link_ALPHA1-4 : angle 1.25921 / 0.69 ( 3) link_BETA1-3 : bond 0.01054 / 0.55 ( 1) link_BETA1-3 : angle 5.58496 / 3.01 ( 3) link_BETA1-4 : bond 0.00931 / 0.47 ( 4) link_BETA1-4 : angle 3.12281 / 1.79 ( 12) link_NAG-ASN : bond 0.00643 / 0.30 ( 13) link_NAG-ASN : angle 2.82002 / 2.43 ( 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 153 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 106 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6470 (OUTLIER) cc_final: 0.5691 (t80) REVERT: A 436 ASP cc_start: 0.6847 (OUTLIER) cc_final: 0.6536 (m-30) REVERT: A 622 PHE cc_start: 0.6264 (t80) cc_final: 0.5727 (m-10) REVERT: A 661 ILE cc_start: 0.7771 (mm) cc_final: 0.7483 (mm) REVERT: A 872 MET cc_start: 0.7935 (mmm) cc_final: 0.7690 (mmm) REVERT: A 1114 MET cc_start: 0.6982 (tmm) cc_final: 0.6491 (tmm) REVERT: A 1133 MET cc_start: 0.7561 (ttm) cc_final: 0.7318 (mtp) REVERT: A 1137 ASN cc_start: 0.8205 (m-40) cc_final: 0.7880 (m110) REVERT: A 1159 MET cc_start: 0.8143 (ttm) cc_final: 0.7940 (ttp) REVERT: A 1220 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7256 (tp) outliers start: 47 outliers final: 28 residues processed: 144 average time/residue: 0.0635 time to fit residues: 14.7712 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 : 0.230 ------------------------------------------------------------------------------- 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 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 1115 VAL Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 99 optimal weight: 0.8980 chunk 5 optimal weight: 30.0000 chunk 2 optimal weight: 50.0000 chunk 83 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 45 optimal weight: 0.0570 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 349 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.166706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.128529 restraints weight = 13818.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.126139 restraints weight = 9022.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.128065 restraints weight = 8408.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.128768 restraints weight = 5288.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129268 restraints weight = 4920.049| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9910 Z= 0.160 Angle : 0.755 10.237 13541 Z= 0.360 Chirality : 0.048 0.333 1573 Planarity : 0.004 0.042 1690 Dihedral : 5.691 55.807 1297 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.48 % Favored : 93.27 % Rotamer: Outliers : 3.86 % Allowed : 17.78 % Favored : 78.36 % 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: -0.46 (0.25), residues: 1188 helix: 0.98 (0.21), residues: 632 sheet: -0.94 (0.58), residues: 81 loop : -2.00 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 116 TYR 0.025 0.001 TYR A 677 PHE 0.028 0.002 PHE A 101 TRP 0.011 0.001 TRP A 833 HIS 0.007 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 9876) covalent geometry : angle 0.72345 / 0.35 (13454) SS BOND : bond 0.00411 / 0.24 ( 15) SS BOND : angle 2.16068 / 1.33 ( 30) hydrogen bonds : bond 0.04203 / 2.77 ( 474) hydrogen bonds : angle 4.72993 / 3.25 ( 1374) link_ALPHA1-4 : bond 0.00483 / 0.25 ( 1) link_ALPHA1-4 : angle 1.25792 / 0.68 ( 3) link_BETA1-3 : bond 0.00607 / 0.32 ( 1) link_BETA1-3 : angle 5.29870 / 2.85 ( 3) link_BETA1-4 : bond 0.00821 / 0.41 ( 4) link_BETA1-4 : angle 3.01035 / 1.74 ( 12) link_NAG-ASN : bond 0.00670 / 0.31 ( 13) link_NAG-ASN : angle 2.97285 / 2.54 ( 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 139 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6429 (OUTLIER) cc_final: 0.5559 (t80) REVERT: A 436 ASP cc_start: 0.6889 (OUTLIER) cc_final: 0.6586 (m-30) REVERT: A 622 PHE cc_start: 0.6327 (t80) cc_final: 0.5732 (m-10) REVERT: A 632 PHE cc_start: 0.7071 (t80) cc_final: 0.6662 (t80) REVERT: A 661 ILE cc_start: 0.7843 (mm) cc_final: 0.7585 (mm) REVERT: A 872 MET cc_start: 0.7919 (mmm) cc_final: 0.7502 (mmt) REVERT: A 1114 MET cc_start: 0.6994 (tmm) cc_final: 0.6402 (tmm) REVERT: A 1133 MET cc_start: 0.7558 (ttm) cc_final: 0.7290 (mtp) REVERT: A 1137 ASN cc_start: 0.8138 (m-40) cc_final: 0.7790 (m110) REVERT: A 1220 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7238 (tp) outliers start: 40 outliers final: 32 residues processed: 133 average time/residue: 0.0621 time to fit residues: 13.0726 Evaluate side-chains 130 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 642 MET 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 776 ILE 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 889 VAL Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 84 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 775 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.169018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.131066 restraints weight = 13698.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.130722 restraints weight = 8665.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.132134 restraints weight = 8529.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.132828 restraints weight = 5114.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133196 restraints weight = 4579.462| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9910 Z= 0.133 Angle : 0.725 10.407 13541 Z= 0.341 Chirality : 0.047 0.442 1573 Planarity : 0.004 0.041 1690 Dihedral : 5.560 55.218 1297 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.69 % Rotamer: Outliers : 4.25 % Allowed : 18.26 % 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: -0.26 (0.25), residues: 1188 helix: 1.10 (0.21), residues: 625 sheet: -0.74 (0.59), residues: 81 loop : -1.82 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.027 0.001 TYR A 677 PHE 0.026 0.001 PHE A 101 TRP 0.017 0.001 TRP A 189 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9876) covalent geometry : angle 0.70064 / 0.33 (13454) SS BOND : bond 0.00385 / 0.23 ( 15) SS BOND : angle 1.88896 / 1.18 ( 30) hydrogen bonds : bond 0.03854 / 2.54 ( 474) hydrogen bonds : angle 4.63522 / 3.18 ( 1374) link_ALPHA1-4 : bond 0.00443 / 0.23 ( 1) link_ALPHA1-4 : angle 1.27584 / 0.70 ( 3) link_BETA1-3 : bond 0.00775 / 0.41 ( 1) link_BETA1-3 : angle 4.90521 / 2.64 ( 3) link_BETA1-4 : bond 0.00880 / 0.44 ( 4) link_BETA1-4 : angle 2.88032 / 1.66 ( 12) link_NAG-ASN : bond 0.00493 / 0.21 ( 13) link_NAG-ASN : angle 2.46727 / 2.28 ( 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 143 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6505 (OUTLIER) cc_final: 0.5590 (t80) REVERT: A 436 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6621 (m-30) REVERT: A 622 PHE cc_start: 0.6333 (t80) cc_final: 0.5791 (m-10) REVERT: A 632 PHE cc_start: 0.7051 (t80) cc_final: 0.6745 (t80) REVERT: A 661 ILE cc_start: 0.7816 (mm) cc_final: 0.7526 (mm) REVERT: A 872 MET cc_start: 0.7983 (mmm) cc_final: 0.7576 (mmm) REVERT: A 1089 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.6904 (tm-30) REVERT: A 1114 MET cc_start: 0.6937 (tmm) cc_final: 0.6350 (tmm) REVERT: A 1133 MET cc_start: 0.7451 (ttm) cc_final: 0.7191 (mtp) REVERT: A 1137 ASN cc_start: 0.8155 (m-40) cc_final: 0.7825 (m110) REVERT: A 1159 MET cc_start: 0.8133 (ttm) cc_final: 0.7826 (ttp) outliers start: 44 outliers final: 29 residues processed: 138 average time/residue: 0.0617 time to fit residues: 13.7338 Evaluate side-chains 124 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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 368 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 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 889 VAL Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1158 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 8 optimal weight: 10.0000 chunk 45 optimal weight: 0.0870 chunk 111 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 27 optimal weight: 0.0010 chunk 91 optimal weight: 0.5980 overall best weight: 0.4966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.170054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.131977 restraints weight = 13897.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.132357 restraints weight = 8577.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133767 restraints weight = 7354.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133990 restraints weight = 4888.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.134350 restraints weight = 4724.396| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9910 Z= 0.119 Angle : 0.700 10.109 13541 Z= 0.329 Chirality : 0.046 0.322 1573 Planarity : 0.004 0.041 1690 Dihedral : 5.376 53.393 1297 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.64 % Favored : 94.11 % Rotamer: Outliers : 3.38 % Allowed : 19.90 % Favored : 76.71 % 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: 1.17 (0.21), residues: 631 sheet: -0.58 (0.61), residues: 81 loop : -1.76 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.022 0.001 TYR A 677 PHE 0.028 0.001 PHE A 736 TRP 0.008 0.001 TRP A 833 HIS 0.006 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 9876) covalent geometry : angle 0.68153 / 0.32 (13454) SS BOND : bond 0.00375 / 0.24 ( 15) SS BOND : angle 1.52319 / 0.97 ( 30) hydrogen bonds : bond 0.03611 / 2.38 ( 474) hydrogen bonds : angle 4.57939 / 3.14 ( 1374) link_ALPHA1-4 : bond 0.00413 / 0.22 ( 1) link_ALPHA1-4 : angle 1.26710 / 0.69 ( 3) link_BETA1-3 : bond 0.00604 / 0.32 ( 1) link_BETA1-3 : angle 4.57760 / 2.46 ( 3) link_BETA1-4 : bond 0.00889 / 0.44 ( 4) link_BETA1-4 : angle 2.75097 / 1.60 ( 12) link_NAG-ASN : bond 0.00503 / 0.23 ( 13) link_NAG-ASN : angle 2.01481 / 1.86 ( 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 139 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.5565 (t80) REVERT: A 436 ASP cc_start: 0.6838 (m-30) cc_final: 0.6489 (m-30) REVERT: A 661 ILE cc_start: 0.7815 (mm) cc_final: 0.7559 (mm) REVERT: A 1114 MET cc_start: 0.6898 (tmm) cc_final: 0.6320 (tmm) REVERT: A 1159 MET cc_start: 0.8211 (ttm) cc_final: 0.7948 (ttp) outliers start: 35 outliers final: 30 residues processed: 137 average time/residue: 0.0662 time to fit residues: 14.4867 Evaluate side-chains 127 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 44 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 925 ASN A1101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.167987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.129294 restraints weight = 13711.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.128961 restraints weight = 8065.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129893 restraints weight = 9056.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130804 restraints weight = 5382.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131710 restraints weight = 4668.714| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3187 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= 0.132 Angle : 0.712 11.189 13541 Z= 0.333 Chirality : 0.046 0.321 1573 Planarity : 0.004 0.041 1690 Dihedral : 5.117 49.834 1295 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.89 % Favored : 93.86 % Rotamer: Outliers : 3.48 % Allowed : 20.77 % Favored : 75.75 % 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: -0.05 (0.25), residues: 1188 helix: 1.26 (0.21), residues: 631 sheet: -0.59 (0.60), residues: 81 loop : -1.74 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.013 0.001 TYR A1037 PHE 0.021 0.001 PHE A 345 TRP 0.008 0.001 TRP A 833 HIS 0.008 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 9876) covalent geometry : angle 0.69379 / 0.33 (13454) SS BOND : bond 0.00478 / 0.32 ( 15) SS BOND : angle 1.68616 / 1.05 ( 30) hydrogen bonds : bond 0.03743 / 2.46 ( 474) hydrogen bonds : angle 4.58823 / 3.15 ( 1374) link_ALPHA1-4 : bond 0.00571 / 0.30 ( 1) link_ALPHA1-4 : angle 1.32161 / 0.72 ( 3) link_BETA1-3 : bond 0.00547 / 0.29 ( 1) link_BETA1-3 : angle 4.37785 / 2.36 ( 3) link_BETA1-4 : bond 0.00908 / 0.46 ( 4) link_BETA1-4 : angle 2.76819 / 1.60 ( 12) link_NAG-ASN : bond 0.00467 / 0.19 ( 13) link_NAG-ASN : angle 1.93890 / 1.80 ( 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 133 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6587 (OUTLIER) cc_final: 0.5505 (t80) REVERT: A 436 ASP cc_start: 0.6892 (m-30) cc_final: 0.6540 (m-30) REVERT: A 1001 MET cc_start: 0.8664 (mmm) cc_final: 0.8423 (mtp) REVERT: A 1114 MET cc_start: 0.6921 (tmm) cc_final: 0.6294 (tmm) outliers start: 36 outliers final: 31 residues processed: 131 average time/residue: 0.0614 time to fit residues: 12.9090 Evaluate side-chains 125 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 112 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 111 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.168000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.129171 restraints weight = 13626.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.127794 restraints weight = 8138.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.128999 restraints weight = 9257.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130014 restraints weight = 5729.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133373 restraints weight = 4985.857| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3247 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 : 0.694 10.640 13541 Z= 0.326 Chirality : 0.046 0.321 1573 Planarity : 0.004 0.041 1690 Dihedral : 5.085 50.004 1295 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.72 % Favored : 94.02 % Rotamer: Outliers : 3.48 % Allowed : 20.58 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z 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: 0.02 (0.25), residues: 1188 helix: 1.30 (0.21), residues: 632 sheet: -0.55 (0.61), residues: 81 loop : -1.70 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.022 0.001 TYR A 102 PHE 0.017 0.001 PHE A 769 TRP 0.008 0.001 TRP A 833 HIS 0.009 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9876) covalent geometry : angle 0.67603 / 0.32 (13454) SS BOND : bond 0.00340 / 0.20 ( 15) SS BOND : angle 1.66976 / 1.04 ( 30) hydrogen bonds : bond 0.03708 / 2.44 ( 474) hydrogen bonds : angle 4.58683 / 3.14 ( 1374) link_ALPHA1-4 : bond 0.00620 / 0.33 ( 1) link_ALPHA1-4 : angle 1.33359 / 0.73 ( 3) link_BETA1-3 : bond 0.00518 / 0.27 ( 1) link_BETA1-3 : angle 4.25588 / 2.29 ( 3) link_BETA1-4 : bond 0.00904 / 0.45 ( 4) link_BETA1-4 : angle 2.75014 / 1.59 ( 12) link_NAG-ASN : bond 0.00474 / 0.20 ( 13) link_NAG-ASN : angle 1.89139 / 1.75 ( 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 133 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.5926 (pttm) cc_final: 0.5439 (tttp) REVERT: A 288 PHE cc_start: 0.6626 (OUTLIER) cc_final: 0.5558 (t80) REVERT: A 436 ASP cc_start: 0.6896 (OUTLIER) cc_final: 0.6526 (m-30) REVERT: A 1001 MET cc_start: 0.8679 (mmm) cc_final: 0.8429 (mtp) REVERT: A 1114 MET cc_start: 0.6973 (tmm) cc_final: 0.6315 (tmm) outliers start: 36 outliers final: 33 residues processed: 129 average time/residue: 0.0650 time to fit residues: 13.4743 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 : 0.325 ------------------------------------------------------------------------------- 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 368 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 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: 0.0170 chunk 88 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.169700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.131005 restraints weight = 13584.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130676 restraints weight = 7903.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.131420 restraints weight = 9000.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.132383 restraints weight = 5381.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135570 restraints weight = 4590.225| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3368 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= 0.121 Angle : 0.682 10.531 13541 Z= 0.319 Chirality : 0.046 0.317 1573 Planarity : 0.004 0.041 1690 Dihedral : 4.986 49.008 1295 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.72 % Favored : 94.11 % Rotamer: Outliers : 3.19 % Allowed : 20.77 % Favored : 76.04 % 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: 1.40 (0.21), residues: 632 sheet: -0.51 (0.61), residues: 81 loop : -1.68 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.020 0.001 TYR A 102 PHE 0.021 0.001 PHE A 632 TRP 0.008 0.001 TRP A 833 HIS 0.008 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 9876) covalent geometry : angle 0.66533 / 0.31 (13454) SS BOND : bond 0.00385 / 0.26 ( 15) SS BOND : angle 1.66301 / 1.03 ( 30) hydrogen bonds : bond 0.03594 / 2.36 ( 474) hydrogen bonds : angle 4.53842 / 3.11 ( 1374) link_ALPHA1-4 : bond 0.00599 / 0.32 ( 1) link_ALPHA1-4 : angle 1.35365 / 0.74 ( 3) link_BETA1-3 : bond 0.00498 / 0.26 ( 1) link_BETA1-3 : angle 3.95918 / 2.12 ( 3) link_BETA1-4 : bond 0.00850 / 0.43 ( 4) link_BETA1-4 : angle 2.66164 / 1.54 ( 12) link_NAG-ASN : bond 0.00470 / 0.21 ( 13) link_NAG-ASN : angle 1.76756 / 1.63 ( 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 135 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6535 (OUTLIER) cc_final: 0.5472 (t80) REVERT: A 436 ASP cc_start: 0.6872 (m-30) cc_final: 0.6490 (m-30) REVERT: A 1001 MET cc_start: 0.8670 (mmm) cc_final: 0.8389 (mtp) REVERT: A 1114 MET cc_start: 0.6944 (tmm) cc_final: 0.6295 (tmm) outliers start: 33 outliers final: 31 residues processed: 132 average time/residue: 0.0626 time to fit residues: 13.2480 Evaluate side-chains 125 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 18 optimal weight: 40.0000 chunk 86 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.169333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.130521 restraints weight = 13731.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130574 restraints weight = 8382.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.131732 restraints weight = 8127.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132344 restraints weight = 5245.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.132764 restraints weight = 4764.899| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.225 9910 Z= 0.249 Angle : 1.043 59.199 13541 Z= 0.573 Chirality : 0.050 0.640 1573 Planarity : 0.006 0.169 1690 Dihedral : 4.990 49.029 1295 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.81 % Favored : 94.02 % Rotamer: Outliers : 3.19 % Allowed : 20.97 % Favored : 75.85 % Cbeta Deviations : 0.18 % 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: 1.40 (0.21), residues: 632 sheet: -0.54 (0.61), residues: 81 loop : -1.67 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.016 0.001 TYR A 102 PHE 0.017 0.001 PHE A 769 TRP 0.007 0.001 TRP A 833 HIS 0.008 0.001 HIS A1042 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.25 ( 9876) covalent geometry : angle 1.03356 / 0.57 (13454) SS BOND : bond 0.00355 / 0.20 ( 15) SS BOND : angle 1.70448 / 1.05 ( 30) hydrogen bonds : bond 0.03634 / 2.39 ( 474) hydrogen bonds : angle 4.53560 / 3.11 ( 1374) link_ALPHA1-4 : bond 0.00621 / 0.33 ( 1) link_ALPHA1-4 : angle 1.34358 / 0.74 ( 3) link_BETA1-3 : bond 0.00492 / 0.26 ( 1) link_BETA1-3 : angle 3.95570 / 2.12 ( 3) link_BETA1-4 : bond 0.00845 / 0.42 ( 4) link_BETA1-4 : angle 2.68048 / 1.55 ( 12) link_NAG-ASN : bond 0.00475 / 0.21 ( 13) link_NAG-ASN : angle 1.76942 / 1.63 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1413.43 seconds wall clock time: 25 minutes 13.02 seconds (1513.02 seconds total)