Starting phenix.real_space_refine on Fri Jul 3 00:23:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tyf_26178/07_2026/7tyf_26178.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyf_26178/07_2026/7tyf_26178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7tyf_26178/07_2026/7tyf_26178.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tyf_26178/07_2026/7tyf_26178.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tyf_26178/07_2026/7tyf_26178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyf_26178/07_2026/7tyf_26178.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tyf_26178/07_2026/7tyf_26178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyf_26178/07_2026/7tyf_26178.map" } resolution = 2.2 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 71 5.16 5 C 6599 2.51 5 N 1730 2.21 5 O 1929 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10331 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1857 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "E" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 759 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 6, 'TRANS': 105} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 87 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 284 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Conformer: "B" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} bond proxies already assigned to first conformer: 265 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2982 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 3, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "R" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 362 Unusual residues: {'NAG': 2, 'P42': 1, 'PLM': 9, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "P" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG P 18 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG P 18 " occ=0.50 Time building chain proxies: 2.09, per 1000 atoms: 0.20 Number of scatterers: 10331 At special positions: 0 Unit cell: (109.56, 98.77, 151.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 71 16.00 P 2 15.00 O 1929 8.00 N 1730 7.00 C 6599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.04 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.04 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 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=1, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 73 " " NAG R 502 " - " ASN R 130 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 271.7 milliseconds 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 13 sheets defined 45.5% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 11 through 40 removed outlier: 3.564A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.945A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.533A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.830A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.627A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 34 through 48 removed outlier: 4.338A pdb=" N CYS E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 41 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 81 removed outlier: 3.748A pdb=" N ARG E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA E 70 " --> pdb=" O TYR E 66 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS E 79 " --> pdb=" O HIS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 100 Processing helix chain 'E' and resid 115 through 143 Proline residue: E 121 - end of helix Proline residue: E 126 - end of helix removed outlier: 3.509A pdb=" N ARG E 143 " --> pdb=" O TRP E 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.500A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 19 Processing helix chain 'R' and resid 44 through 62 removed outlier: 3.628A pdb=" N MET R 48 " --> pdb=" O GLY R 44 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP R 57 " --> pdb=" O TYR R 53 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU R 62 " --> pdb=" O ARG R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 137 removed outlier: 4.512A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE R 137 " --> pdb=" O MET R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.547A pdb=" N ASN R 144 " --> pdb=" O GLU R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 204 Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.577A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.689A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 405 Processing helix chain 'R' and resid 406 through 409 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.464A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.875A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.814A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.746A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.685A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.639A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.537A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.707A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.114A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 71 through 72 removed outlier: 3.562A pdb=" N CYS R 72 " --> pdb=" O THR R 85 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR R 85 " --> pdb=" O CYS R 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'R' and resid 90 through 94 528 hydrogen bonds defined for protein. 1489 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: 1.17 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1691 1.32 - 1.45: 2895 1.45 - 1.58: 5789 1.58 - 1.70: 4 1.70 - 1.83: 99 Bond restraints: 10478 Sorted by residual: bond pdb=" N ILE E 106 " pdb=" CA ILE E 106 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.26e-02 6.30e+03 8.20e+00 bond pdb=" N ASP E 58 " pdb=" CA ASP E 58 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.22e-02 6.72e+03 6.95e+00 bond pdb=" N THR E 54 " pdb=" CA THR E 54 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.53e+00 bond pdb=" OBN P42 R 510 " pdb=" PBM P42 R 510 " ideal model delta sigma weight residual 1.657 1.607 0.050 2.00e-02 2.50e+03 6.36e+00 bond pdb=" N SER E 103 " pdb=" CA SER E 103 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.17e-02 7.31e+03 6.15e+00 ... (remaining 10473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 13960 1.90 - 3.81: 184 3.81 - 5.71: 19 5.71 - 7.62: 1 7.62 - 9.52: 2 Bond angle restraints: 14166 Sorted by residual: angle pdb=" N ILE E 118 " pdb=" CA ILE E 118 " pdb=" C ILE E 118 " ideal model delta sigma weight residual 112.96 109.64 3.32 1.00e+00 1.00e+00 1.10e+01 angle pdb=" N VAL B 90 " pdb=" CA VAL B 90 " pdb=" C VAL B 90 " ideal model delta sigma weight residual 111.81 109.07 2.74 8.60e-01 1.35e+00 1.02e+01 angle pdb=" O11 PTY R 514 " pdb=" P1 PTY R 514 " pdb=" O14 PTY R 514 " ideal model delta sigma weight residual 92.90 102.42 -9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" N THR E 54 " pdb=" CA THR E 54 " pdb=" C THR E 54 " ideal model delta sigma weight residual 113.16 109.37 3.79 1.24e+00 6.50e-01 9.34e+00 angle pdb=" CA LEU E 55 " pdb=" C LEU E 55 " pdb=" O LEU E 55 " ideal model delta sigma weight residual 120.55 117.60 2.95 1.06e+00 8.90e-01 7.72e+00 ... (remaining 14161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.66: 5924 26.66 - 53.32: 231 53.32 - 79.98: 44 79.98 - 106.64: 2 106.64 - 133.30: 2 Dihedral angle restraints: 6203 sinusoidal: 2511 harmonic: 3692 Sorted by residual: dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual -86.00 -21.95 -64.05 1 1.00e+01 1.00e-02 5.40e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual 93.00 147.10 -54.10 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 6200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1140 0.041 - 0.082: 313 0.082 - 0.123: 96 0.123 - 0.164: 6 0.164 - 0.204: 3 Chirality restraints: 1558 Sorted by residual: chirality pdb=" CBE P42 R 510 " pdb=" CAB P42 R 510 " pdb=" CBK P42 R 510 " pdb=" OBD P42 R 510 " both_signs ideal model delta sigma weight residual False -2.32 -2.53 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE E 106 " pdb=" N ILE E 106 " pdb=" C ILE E 106 " pdb=" CB ILE E 106 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" C1 NAG R 502 " pdb=" ND2 ASN R 130 " pdb=" C2 NAG R 502 " pdb=" O5 NAG R 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.31e-01 ... (remaining 1555 not shown) Planarity restraints: 1777 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN R 73 " -0.016 2.00e-02 2.50e+03 1.48e-02 2.72e+00 pdb=" CG ASN R 73 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN R 73 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN R 73 " 0.011 2.00e-02 2.50e+03 pdb=" C1 NAG R 501 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.88e+00 pdb=" N PRO B 236 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 303 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.84e+00 pdb=" N PRO R 304 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO R 304 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 304 " -0.019 5.00e-02 4.00e+02 ... (remaining 1774 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1828 2.77 - 3.30: 9967 3.30 - 3.83: 18014 3.83 - 4.37: 22208 4.37 - 4.90: 36257 Nonbonded interactions: 88274 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.234 3.040 nonbonded pdb=" O LEU P 16 " pdb=" OG SER P 20 " model vdw 2.274 3.040 nonbonded pdb=" O TYR A 318 " pdb=" NH1 ARG A 336 " model vdw 2.292 3.120 nonbonded pdb=" OD1 ASP N 106 " pdb=" O HOH N 201 " model vdw 2.294 3.040 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.300 3.120 ... (remaining 88269 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.100 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 : 0.004 0.106 10490 Z= 0.232 Angle : 0.576 9.523 14190 Z= 0.325 Chirality : 0.042 0.204 1558 Planarity : 0.003 0.034 1775 Dihedral : 14.451 133.305 3792 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.87 % Allowed : 10.84 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.73 (0.20), residues: 1251 helix: -1.23 (0.18), residues: 503 sheet: -0.21 (0.32), residues: 226 loop : -1.32 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 213 TYR 0.009 0.001 TYR R 65 PHE 0.012 0.001 PHE B 151 TRP 0.016 0.001 TRP A 234 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.21 (10478) covalent geometry : angle 0.57163 / 0.32 (14166) SS BOND : bond 0.00351 / 0.24 ( 9) SS BOND : angle 0.92906 / 0.57 ( 18) hydrogen bonds : bond 0.22690 / 15.21 ( 528) hydrogen bonds : angle 7.85798 / 5.52 ( 1489) Misc. bond : bond 0.10594 / 5.58 ( 1) link_NAG-ASN : bond 0.00934 / 0.47 ( 2) link_NAG-ASN : angle 3.05914 / 1.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 0.239 Fit side-chains REVERT: A 370 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6604 (tp30) REVERT: B 19 ARG cc_start: 0.7556 (ttp-110) cc_final: 0.7274 (ttm-80) REVERT: B 197 ARG cc_start: 0.7610 (mmm-85) cc_final: 0.7274 (mmm160) REVERT: B 214 ARG cc_start: 0.7199 (mmt180) cc_final: 0.6861 (mmt180) REVERT: P 23 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5881 (mp) REVERT: R 130 ASN cc_start: 0.3481 (OUTLIER) cc_final: 0.2829 (t0) REVERT: R 167 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7956 (tt) REVERT: R 328 ARG cc_start: 0.6994 (mtt180) cc_final: 0.6526 (mtt-85) outliers start: 9 outliers final: 4 residues processed: 193 average time/residue: 0.6115 time to fit residues: 125.5125 Evaluate side-chains 172 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain R residue 167 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN A 294 GLN B 16 ASN B 75 GLN B 88 ASN B 155 ASN N 3 GLN N 13 GLN N 77 ASN P 22 ASN R 201 HIS R 318 ASN R 365 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.193670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.148825 restraints weight = 15467.417| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 3.48 r_work: 0.3058 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10490 Z= 0.167 Angle : 0.602 7.617 14190 Z= 0.326 Chirality : 0.045 0.150 1558 Planarity : 0.005 0.041 1775 Dihedral : 8.471 94.833 1613 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.71 % Allowed : 12.29 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.23), residues: 1251 helix: 1.01 (0.22), residues: 510 sheet: -0.16 (0.32), residues: 239 loop : -1.02 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 219 TYR 0.022 0.002 TYR R 56 PHE 0.014 0.002 PHE R 269 TRP 0.021 0.002 TRP A 234 HIS 0.006 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (10478) covalent geometry : angle 0.60015 / 0.33 (14166) SS BOND : bond 0.00414 / 0.24 ( 9) SS BOND : angle 1.09230 / 0.64 ( 18) hydrogen bonds : bond 0.05871 / 3.89 ( 528) hydrogen bonds : angle 5.15482 / 3.65 ( 1489) Misc. bond : bond 0.00011 / 0.01 ( 1) link_NAG-ASN : bond 0.00505 / 0.27 ( 2) link_NAG-ASN : angle 1.51594 / 0.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7129 (mtm-85) cc_final: 0.6399 (mpt180) REVERT: A 31 GLN cc_start: 0.8110 (tp40) cc_final: 0.7887 (tp40) REVERT: A 370 GLU cc_start: 0.7549 (mm-30) cc_final: 0.6889 (mp0) REVERT: B 19 ARG cc_start: 0.7811 (ttp-110) cc_final: 0.7236 (ttm-80) REVERT: B 44 GLN cc_start: 0.7038 (OUTLIER) cc_final: 0.6621 (pt0) REVERT: B 197 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.7774 (mmm160) REVERT: B 214 ARG cc_start: 0.7489 (mmt180) cc_final: 0.7026 (mmt180) REVERT: G 13 ARG cc_start: 0.6347 (ttm170) cc_final: 0.6075 (ttm110) REVERT: G 29 LYS cc_start: 0.8698 (mmtm) cc_final: 0.8355 (mmmt) REVERT: R 140 GLU cc_start: 0.6296 (mm-30) cc_final: 0.5792 (mp0) REVERT: R 171 VAL cc_start: 0.7403 (t) cc_final: 0.7057 (m) REVERT: R 174 ARG cc_start: 0.6404 (mtp180) cc_final: 0.6150 (mtp180) REVERT: R 258 ARG cc_start: 0.6964 (mtm180) cc_final: 0.6118 (mtt-85) REVERT: R 321 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7735 (ttt-90) REVERT: R 328 ARG cc_start: 0.7331 (mtt180) cc_final: 0.6845 (mtt-85) REVERT: R 343 LYS cc_start: 0.8019 (tttt) cc_final: 0.7419 (tmmt) outliers start: 28 outliers final: 13 residues processed: 196 average time/residue: 0.6112 time to fit residues: 127.5908 Evaluate side-chains 182 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 11 optimal weight: 0.0970 chunk 25 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN E 140 GLN N 3 GLN N 13 GLN N 77 ASN R 257 GLN R 365 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.194395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.162196 restraints weight = 13952.297| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.09 r_work: 0.3077 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10490 Z= 0.139 Angle : 0.557 7.543 14190 Z= 0.300 Chirality : 0.043 0.162 1558 Planarity : 0.004 0.041 1775 Dihedral : 7.780 75.681 1607 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.71 % Allowed : 12.78 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.24), residues: 1251 helix: 1.57 (0.23), residues: 515 sheet: -0.05 (0.32), residues: 237 loop : -0.79 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.021 0.002 TYR R 56 PHE 0.013 0.001 PHE B 151 TRP 0.021 0.002 TRP A 234 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (10478) covalent geometry : angle 0.55630 / 0.30 (14166) SS BOND : bond 0.00366 / 0.22 ( 9) SS BOND : angle 0.91666 / 0.56 ( 18) hydrogen bonds : bond 0.05152 / 3.42 ( 528) hydrogen bonds : angle 4.83959 / 3.43 ( 1489) Misc. bond : bond 0.00025 / 0.01 ( 1) link_NAG-ASN : bond 0.00366 / 0.19 ( 2) link_NAG-ASN : angle 1.17894 / 0.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7116 (mtm-85) cc_final: 0.6554 (mpt180) REVERT: A 35 GLN cc_start: 0.7716 (tm-30) cc_final: 0.7428 (mm110) REVERT: A 296 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6804 (mp) REVERT: A 370 GLU cc_start: 0.7601 (mm-30) cc_final: 0.6834 (OUTLIER) REVERT: B 12 GLU cc_start: 0.7024 (tp30) cc_final: 0.6650 (tt0) REVERT: B 19 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7413 (ttm-80) REVERT: B 44 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6624 (pt0) REVERT: B 197 ARG cc_start: 0.8309 (mmm-85) cc_final: 0.7789 (mmm160) REVERT: B 214 ARG cc_start: 0.7496 (mmt180) cc_final: 0.7106 (mmt180) REVERT: R 140 GLU cc_start: 0.6311 (mm-30) cc_final: 0.5955 (mp0) REVERT: R 171 VAL cc_start: 0.7476 (t) cc_final: 0.7150 (m) REVERT: R 174 ARG cc_start: 0.6501 (mtp180) cc_final: 0.6265 (mtp180) REVERT: R 328 ARG cc_start: 0.7307 (mtt180) cc_final: 0.6832 (mtt-85) REVERT: R 343 LYS cc_start: 0.8110 (tttt) cc_final: 0.7561 (tmmt) REVERT: R 364 SER cc_start: 0.8125 (m) cc_final: 0.7372 (p) outliers start: 28 outliers final: 16 residues processed: 188 average time/residue: 0.5983 time to fit residues: 119.6859 Evaluate side-chains 184 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 92 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 340 ASN E 140 GLN N 3 GLN N 13 GLN R 257 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.194376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.150256 restraints weight = 14818.674| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.43 r_work: 0.3067 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10490 Z= 0.138 Angle : 0.557 7.835 14190 Z= 0.298 Chirality : 0.043 0.170 1558 Planarity : 0.004 0.041 1775 Dihedral : 7.777 76.831 1606 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.71 % Allowed : 13.36 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.67 (0.24), residues: 1251 helix: 1.80 (0.23), residues: 515 sheet: -0.02 (0.32), residues: 235 loop : -0.71 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 258 TYR 0.020 0.002 TYR R 56 PHE 0.014 0.001 PHE B 151 TRP 0.021 0.002 TRP A 234 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (10478) covalent geometry : angle 0.55561 / 0.30 (14166) SS BOND : bond 0.00375 / 0.22 ( 9) SS BOND : angle 1.01873 / 0.64 ( 18) hydrogen bonds : bond 0.04931 / 3.27 ( 528) hydrogen bonds : angle 4.71774 / 3.35 ( 1489) Misc. bond : bond 0.00025 / 0.01 ( 1) link_NAG-ASN : bond 0.00369 / 0.19 ( 2) link_NAG-ASN : angle 1.45141 / 0.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7099 (mtm-85) cc_final: 0.6489 (mpt180) REVERT: A 27 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7832 (tp30) REVERT: A 35 GLN cc_start: 0.7646 (tm-30) cc_final: 0.7334 (mm110) REVERT: A 296 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6525 (mp) REVERT: A 370 GLU cc_start: 0.7550 (mm-30) cc_final: 0.6750 (OUTLIER) REVERT: B 12 GLU cc_start: 0.6954 (tp30) cc_final: 0.6485 (tt0) REVERT: B 19 ARG cc_start: 0.7796 (ttp-110) cc_final: 0.7214 (ttm-80) REVERT: B 44 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6595 (pt0) REVERT: B 197 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.7771 (mmm160) REVERT: B 214 ARG cc_start: 0.7451 (mmt180) cc_final: 0.7012 (mmt180) REVERT: E 40 CYS cc_start: 0.2498 (OUTLIER) cc_final: 0.1984 (p) REVERT: R 90 LEU cc_start: 0.2138 (OUTLIER) cc_final: 0.1194 (pt) REVERT: R 140 GLU cc_start: 0.6058 (mm-30) cc_final: 0.5654 (mp0) REVERT: R 171 VAL cc_start: 0.7313 (t) cc_final: 0.6982 (m) REVERT: R 174 ARG cc_start: 0.6420 (mtp180) cc_final: 0.6158 (mtp180) REVERT: R 254 THR cc_start: 0.6980 (m) cc_final: 0.6459 (p) REVERT: R 264 LEU cc_start: 0.7941 (tp) cc_final: 0.7585 (mt) REVERT: R 328 ARG cc_start: 0.7200 (mtt180) cc_final: 0.6703 (mtt-85) REVERT: R 343 LYS cc_start: 0.8021 (tttt) cc_final: 0.7412 (tmmt) REVERT: R 364 SER cc_start: 0.8078 (m) cc_final: 0.7321 (p) outliers start: 28 outliers final: 17 residues processed: 185 average time/residue: 0.6454 time to fit residues: 126.7032 Evaluate side-chains 185 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 60 optimal weight: 0.0770 chunk 82 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 32 GLN B 266 HIS B 340 ASN E 140 GLN N 3 GLN R 208 ASN R 257 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.193596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.154757 restraints weight = 17182.709| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.76 r_work: 0.3057 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10490 Z= 0.157 Angle : 0.589 7.902 14190 Z= 0.314 Chirality : 0.044 0.177 1558 Planarity : 0.004 0.041 1775 Dihedral : 8.202 78.663 1606 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.71 % Allowed : 13.94 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.65 (0.24), residues: 1251 helix: 1.79 (0.23), residues: 516 sheet: -0.02 (0.32), residues: 235 loop : -0.74 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 347 TYR 0.017 0.002 TYR R 56 PHE 0.014 0.001 PHE B 151 TRP 0.022 0.002 TRP A 234 HIS 0.006 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (10478) covalent geometry : angle 0.58648 / 0.31 (14166) SS BOND : bond 0.00445 / 0.26 ( 9) SS BOND : angle 1.24068 / 0.82 ( 18) hydrogen bonds : bond 0.05181 / 3.44 ( 528) hydrogen bonds : angle 4.78251 / 3.39 ( 1489) Misc. bond : bond 0.00036 / 0.02 ( 1) link_NAG-ASN : bond 0.00435 / 0.23 ( 2) link_NAG-ASN : angle 1.79671 / 0.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7891 (tp30) REVERT: A 296 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6556 (mp) REVERT: A 300 LYS cc_start: 0.5096 (OUTLIER) cc_final: 0.4732 (mttm) REVERT: A 370 GLU cc_start: 0.7601 (mm-30) cc_final: 0.6801 (tp30) REVERT: B 12 GLU cc_start: 0.7024 (tp30) cc_final: 0.6568 (tt0) REVERT: B 19 ARG cc_start: 0.7835 (ttp-110) cc_final: 0.7316 (ttm-80) REVERT: B 44 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6574 (pt0) REVERT: B 197 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.7799 (mmm160) REVERT: B 214 ARG cc_start: 0.7483 (mmt180) cc_final: 0.7044 (mmt180) REVERT: B 304 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7913 (ttp-170) REVERT: E 40 CYS cc_start: 0.2610 (OUTLIER) cc_final: 0.2105 (p) REVERT: G 13 ARG cc_start: 0.6316 (ttm170) cc_final: 0.5984 (ttm110) REVERT: R 48 MET cc_start: 0.4487 (ptp) cc_final: 0.3390 (ttt) REVERT: R 90 LEU cc_start: 0.2120 (OUTLIER) cc_final: 0.1168 (pt) REVERT: R 140 GLU cc_start: 0.6189 (mm-30) cc_final: 0.5784 (mp0) REVERT: R 171 VAL cc_start: 0.7359 (t) cc_final: 0.7025 (m) REVERT: R 254 THR cc_start: 0.6993 (m) cc_final: 0.6485 (p) REVERT: R 264 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7689 (mt) REVERT: R 328 ARG cc_start: 0.7289 (mtt180) cc_final: 0.6807 (mtt-85) REVERT: R 343 LYS cc_start: 0.8071 (tttt) cc_final: 0.7490 (tmmt) REVERT: R 364 SER cc_start: 0.8107 (m) cc_final: 0.7349 (p) REVERT: R 367 MET cc_start: 0.5384 (tmm) cc_final: 0.5144 (tmm) REVERT: R 368 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6710 (tp) outliers start: 28 outliers final: 15 residues processed: 189 average time/residue: 0.6944 time to fit residues: 139.3577 Evaluate side-chains 186 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 35 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 266 HIS B 340 ASN E 140 GLN N 3 GLN R 257 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.192707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.130476 restraints weight = 10857.941| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.70 r_work: 0.3161 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10490 Z= 0.182 Angle : 0.622 8.336 14190 Z= 0.332 Chirality : 0.046 0.182 1558 Planarity : 0.004 0.041 1775 Dihedral : 8.715 82.536 1606 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.81 % Allowed : 14.33 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1251 helix: 1.79 (0.23), residues: 509 sheet: -0.09 (0.32), residues: 238 loop : -0.71 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 347 TYR 0.016 0.002 TYR R 56 PHE 0.015 0.002 PHE R 269 TRP 0.024 0.002 TRP A 234 HIS 0.007 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (10478) covalent geometry : angle 0.61975 / 0.33 (14166) SS BOND : bond 0.00513 / 0.30 ( 9) SS BOND : angle 1.33928 / 0.86 ( 18) hydrogen bonds : bond 0.05475 / 3.65 ( 528) hydrogen bonds : angle 4.87889 / 3.45 ( 1489) Misc. bond : bond 0.00039 / 0.02 ( 1) link_NAG-ASN : bond 0.00459 / 0.24 ( 2) link_NAG-ASN : angle 1.93727 / 0.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.427 Fit side-chains REVERT: A 27 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7817 (tp30) REVERT: A 296 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6631 (mp) REVERT: A 300 LYS cc_start: 0.5461 (OUTLIER) cc_final: 0.4970 (mttm) REVERT: B 19 ARG cc_start: 0.7805 (ttp-110) cc_final: 0.7225 (ttm-80) REVERT: B 44 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6644 (pt0) REVERT: B 197 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.7785 (mmm160) REVERT: B 214 ARG cc_start: 0.7529 (mmt180) cc_final: 0.7015 (mmt180) REVERT: B 304 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7917 (ttp-170) REVERT: E 40 CYS cc_start: 0.2518 (OUTLIER) cc_final: 0.1935 (p) REVERT: G 13 ARG cc_start: 0.6406 (ttm170) cc_final: 0.6083 (ttm110) REVERT: G 29 LYS cc_start: 0.8706 (mmtm) cc_final: 0.8387 (mmmt) REVERT: R 48 MET cc_start: 0.4331 (ptp) cc_final: 0.3358 (ttt) REVERT: R 90 LEU cc_start: 0.2069 (OUTLIER) cc_final: 0.1156 (pt) REVERT: R 140 GLU cc_start: 0.6352 (mm-30) cc_final: 0.5923 (mp0) REVERT: R 171 VAL cc_start: 0.7339 (t) cc_final: 0.6993 (m) REVERT: R 254 THR cc_start: 0.7090 (m) cc_final: 0.6502 (p) REVERT: R 264 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7702 (mt) REVERT: R 328 ARG cc_start: 0.7283 (mtt180) cc_final: 0.6761 (mtt-85) REVERT: R 343 LYS cc_start: 0.8029 (tttt) cc_final: 0.7417 (tmmt) REVERT: R 364 SER cc_start: 0.8122 (m) cc_final: 0.7390 (p) REVERT: R 367 MET cc_start: 0.5451 (tmm) cc_final: 0.5204 (tmm) REVERT: R 368 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6773 (tp) outliers start: 29 outliers final: 15 residues processed: 185 average time/residue: 0.7081 time to fit residues: 138.8215 Evaluate side-chains 182 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 37 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 266 HIS B 340 ASN N 3 GLN R 257 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.193366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.159681 restraints weight = 15614.278| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.22 r_work: 0.3067 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10490 Z= 0.162 Angle : 0.603 8.280 14190 Z= 0.319 Chirality : 0.044 0.189 1558 Planarity : 0.004 0.041 1775 Dihedral : 8.584 84.539 1604 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.19 % Allowed : 14.04 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.24), residues: 1251 helix: 1.88 (0.23), residues: 510 sheet: -0.09 (0.31), residues: 237 loop : -0.75 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 347 TYR 0.012 0.002 TYR P 37 PHE 0.015 0.001 PHE B 151 TRP 0.023 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (10478) covalent geometry : angle 0.60097 / 0.32 (14166) SS BOND : bond 0.00483 / 0.29 ( 9) SS BOND : angle 1.23709 / 0.78 ( 18) hydrogen bonds : bond 0.05157 / 3.43 ( 528) hydrogen bonds : angle 4.78186 / 3.38 ( 1489) Misc. bond : bond 0.00023 / 0.01 ( 1) link_NAG-ASN : bond 0.00469 / 0.25 ( 2) link_NAG-ASN : angle 1.66688 / 0.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.260 Fit side-chains REVERT: A 27 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: A 296 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6627 (mp) REVERT: A 300 LYS cc_start: 0.5280 (OUTLIER) cc_final: 0.4818 (mttm) REVERT: A 370 GLU cc_start: 0.7640 (mm-30) cc_final: 0.6914 (mm-30) REVERT: B 9 GLN cc_start: 0.6548 (OUTLIER) cc_final: 0.6179 (mt0) REVERT: B 12 GLU cc_start: 0.6883 (tp30) cc_final: 0.6539 (tt0) REVERT: B 19 ARG cc_start: 0.7855 (ttp-110) cc_final: 0.7315 (ttm-80) REVERT: B 44 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.6637 (pt0) REVERT: B 197 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.7782 (mmm160) REVERT: B 214 ARG cc_start: 0.7525 (mmt180) cc_final: 0.7048 (mmt180) REVERT: B 304 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7916 (ttp-170) REVERT: E 40 CYS cc_start: 0.2444 (OUTLIER) cc_final: 0.2025 (p) REVERT: G 13 ARG cc_start: 0.6308 (ttm170) cc_final: 0.5983 (ttm110) REVERT: G 29 LYS cc_start: 0.8711 (mmtm) cc_final: 0.8399 (mmmt) REVERT: R 48 MET cc_start: 0.4569 (ptp) cc_final: 0.3623 (ttt) REVERT: R 90 LEU cc_start: 0.2237 (OUTLIER) cc_final: 0.1296 (pt) REVERT: R 120 LYS cc_start: 0.5362 (OUTLIER) cc_final: 0.5016 (mmtm) REVERT: R 140 GLU cc_start: 0.6305 (mm-30) cc_final: 0.5944 (mp0) REVERT: R 171 VAL cc_start: 0.7378 (t) cc_final: 0.7028 (m) REVERT: R 174 ARG cc_start: 0.6564 (mtp180) cc_final: 0.6284 (mtp180) REVERT: R 254 THR cc_start: 0.7016 (m) cc_final: 0.6520 (p) REVERT: R 264 LEU cc_start: 0.8046 (tp) cc_final: 0.7745 (mt) REVERT: R 328 ARG cc_start: 0.7309 (mtt180) cc_final: 0.6826 (mtt-85) REVERT: R 343 LYS cc_start: 0.8086 (tttt) cc_final: 0.7508 (tmmt) REVERT: R 364 SER cc_start: 0.8106 (m) cc_final: 0.7397 (p) REVERT: R 367 MET cc_start: 0.5430 (tmm) cc_final: 0.5195 (tmm) REVERT: R 368 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6773 (tp) outliers start: 33 outliers final: 17 residues processed: 192 average time/residue: 0.7199 time to fit residues: 146.5408 Evaluate side-chains 190 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 85 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 266 HIS B 340 ASN E 140 GLN N 3 GLN R 257 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.192574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.152755 restraints weight = 17777.860| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.90 r_work: 0.3047 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10490 Z= 0.186 Angle : 0.651 9.939 14190 Z= 0.344 Chirality : 0.046 0.193 1558 Planarity : 0.004 0.041 1775 Dihedral : 9.073 88.573 1604 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.10 % Allowed : 14.23 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.66 (0.24), residues: 1251 helix: 1.78 (0.23), residues: 509 sheet: 0.00 (0.31), residues: 242 loop : -0.70 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 347 TYR 0.016 0.002 TYR R 284 PHE 0.016 0.002 PHE R 269 TRP 0.024 0.002 TRP A 234 HIS 0.007 0.002 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.19 (10478) covalent geometry : angle 0.64217 / 0.34 (14166) SS BOND : bond 0.00599 / 0.39 ( 9) SS BOND : angle 1.30716 / 0.78 ( 18) hydrogen bonds : bond 0.05505 / 3.67 ( 528) hydrogen bonds : angle 4.87539 / 3.45 ( 1489) Misc. bond : bond 0.00035 / 0.02 ( 1) link_NAG-ASN : bond 0.00568 / 0.29 ( 2) link_NAG-ASN : angle 4.94119 / 2.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.409 Fit side-chains REVERT: A 27 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7891 (tp30) REVERT: A 296 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6676 (mp) REVERT: A 300 LYS cc_start: 0.5414 (OUTLIER) cc_final: 0.4926 (mttm) REVERT: B 9 GLN cc_start: 0.6531 (OUTLIER) cc_final: 0.6201 (mt0) REVERT: B 12 GLU cc_start: 0.6884 (tp30) cc_final: 0.6553 (tt0) REVERT: B 19 ARG cc_start: 0.7858 (ttp-110) cc_final: 0.7328 (ttm-80) REVERT: B 44 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6614 (pt0) REVERT: B 197 ARG cc_start: 0.8311 (mmm-85) cc_final: 0.7757 (mmm160) REVERT: B 214 ARG cc_start: 0.7503 (mmt180) cc_final: 0.7023 (mmt180) REVERT: B 304 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7924 (ttp-170) REVERT: E 40 CYS cc_start: 0.2446 (OUTLIER) cc_final: 0.2021 (p) REVERT: G 13 ARG cc_start: 0.6402 (ttm170) cc_final: 0.6077 (ttm110) REVERT: G 29 LYS cc_start: 0.8751 (mmtm) cc_final: 0.8442 (mmmt) REVERT: R 48 MET cc_start: 0.4580 (ptp) cc_final: 0.3677 (ttt) REVERT: R 90 LEU cc_start: 0.2095 (OUTLIER) cc_final: 0.1171 (pt) REVERT: R 120 LYS cc_start: 0.5305 (OUTLIER) cc_final: 0.4969 (mmtm) REVERT: R 140 GLU cc_start: 0.6374 (mm-30) cc_final: 0.5975 (mp0) REVERT: R 171 VAL cc_start: 0.7410 (t) cc_final: 0.7089 (m) REVERT: R 254 THR cc_start: 0.7147 (m) cc_final: 0.6588 (p) REVERT: R 264 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7751 (mt) REVERT: R 328 ARG cc_start: 0.7328 (mtt180) cc_final: 0.6831 (mtt-85) REVERT: R 343 LYS cc_start: 0.8086 (tttt) cc_final: 0.7513 (tmmt) REVERT: R 364 SER cc_start: 0.8116 (m) cc_final: 0.7422 (p) REVERT: R 367 MET cc_start: 0.5438 (tmm) cc_final: 0.5228 (tmm) REVERT: R 368 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6768 (tp) outliers start: 32 outliers final: 18 residues processed: 185 average time/residue: 0.7369 time to fit residues: 144.6343 Evaluate side-chains 188 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 59 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 43 optimal weight: 6.9990 chunk 81 optimal weight: 0.1980 chunk 78 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 266 HIS B 340 ASN N 3 GLN R 257 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.194887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131189 restraints weight = 13191.397| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.01 r_work: 0.3177 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10490 Z= 0.126 Angle : 0.570 8.958 14190 Z= 0.298 Chirality : 0.042 0.194 1558 Planarity : 0.004 0.040 1775 Dihedral : 8.432 87.474 1604 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.71 % Allowed : 14.71 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.90 (0.24), residues: 1251 helix: 2.04 (0.23), residues: 515 sheet: 0.08 (0.32), residues: 239 loop : -0.65 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 347 TYR 0.012 0.001 TYR R 56 PHE 0.014 0.001 PHE B 151 TRP 0.020 0.002 TRP A 234 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (10478) covalent geometry : angle 0.56385 / 0.30 (14166) SS BOND : bond 0.00410 / 0.29 ( 9) SS BOND : angle 1.05288 / 0.64 ( 18) hydrogen bonds : bond 0.04610 / 3.06 ( 528) hydrogen bonds : angle 4.60858 / 3.26 ( 1489) Misc. bond : bond 0.00019 / 0.01 ( 1) link_NAG-ASN : bond 0.00416 / 0.21 ( 2) link_NAG-ASN : angle 3.63422 / 1.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7755 (tp30) REVERT: A 35 GLN cc_start: 0.7594 (tm-30) cc_final: 0.7238 (mm110) REVERT: A 296 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6565 (mp) REVERT: A 300 LYS cc_start: 0.5222 (OUTLIER) cc_final: 0.4869 (mttm) REVERT: A 370 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6774 (mm-30) REVERT: B 9 GLN cc_start: 0.6531 (OUTLIER) cc_final: 0.6181 (mt0) REVERT: B 12 GLU cc_start: 0.6872 (tp30) cc_final: 0.6471 (tt0) REVERT: B 19 ARG cc_start: 0.7747 (ttp-110) cc_final: 0.7130 (ttm-80) REVERT: B 197 ARG cc_start: 0.8344 (mmm-85) cc_final: 0.7724 (mmm160) REVERT: B 214 ARG cc_start: 0.7486 (mmt180) cc_final: 0.7045 (mmt180) REVERT: B 215 GLU cc_start: 0.7588 (mp0) cc_final: 0.7216 (mt-10) REVERT: B 304 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7923 (ttp-170) REVERT: E 40 CYS cc_start: 0.2571 (OUTLIER) cc_final: 0.1990 (p) REVERT: G 13 ARG cc_start: 0.6293 (ttm170) cc_final: 0.5931 (ttm110) REVERT: G 29 LYS cc_start: 0.8565 (mmtm) cc_final: 0.8209 (mmmt) REVERT: R 48 MET cc_start: 0.4224 (ptp) cc_final: 0.3460 (ttt) REVERT: R 90 LEU cc_start: 0.2048 (OUTLIER) cc_final: 0.1190 (pt) REVERT: R 120 LYS cc_start: 0.5247 (OUTLIER) cc_final: 0.4960 (mmtm) REVERT: R 140 GLU cc_start: 0.6284 (mm-30) cc_final: 0.5869 (mp0) REVERT: R 171 VAL cc_start: 0.7258 (t) cc_final: 0.6898 (m) REVERT: R 254 THR cc_start: 0.6949 (m) cc_final: 0.6413 (p) REVERT: R 264 LEU cc_start: 0.7979 (tp) cc_final: 0.7659 (mt) REVERT: R 328 ARG cc_start: 0.7175 (mtt180) cc_final: 0.6670 (mtt-85) REVERT: R 343 LYS cc_start: 0.7976 (tttt) cc_final: 0.7356 (tmmt) REVERT: R 364 SER cc_start: 0.8062 (m) cc_final: 0.7353 (p) REVERT: R 367 MET cc_start: 0.5281 (tmm) cc_final: 0.5071 (tmm) REVERT: R 368 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6686 (tp) outliers start: 28 outliers final: 14 residues processed: 189 average time/residue: 0.6907 time to fit residues: 138.5223 Evaluate side-chains 186 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 104 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 266 HIS B 340 ASN E 140 GLN N 13 GLN R 257 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.193057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.143715 restraints weight = 13213.157| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.30 r_work: 0.3206 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10490 Z= 0.173 Angle : 0.636 9.003 14190 Z= 0.335 Chirality : 0.045 0.196 1558 Planarity : 0.004 0.041 1775 Dihedral : 9.023 87.883 1604 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.32 % Allowed : 15.30 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.79 (0.24), residues: 1251 helix: 1.93 (0.23), residues: 509 sheet: 0.01 (0.31), residues: 242 loop : -0.65 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.013 0.002 TYR R 284 PHE 0.015 0.002 PHE R 269 TRP 0.024 0.002 TRP A 234 HIS 0.006 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (10478) covalent geometry : angle 0.63042 / 0.33 (14166) SS BOND : bond 0.00544 / 0.35 ( 9) SS BOND : angle 1.30450 / 0.80 ( 18) hydrogen bonds : bond 0.05300 / 3.53 ( 528) hydrogen bonds : angle 4.81856 / 3.40 ( 1489) Misc. bond : bond 0.00037 / 0.02 ( 1) link_NAG-ASN : bond 0.00452 / 0.23 ( 2) link_NAG-ASN : angle 3.63096 / 1.75 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.383 Fit side-chains REVERT: A 27 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7848 (tp30) REVERT: A 296 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6619 (mp) REVERT: A 300 LYS cc_start: 0.5313 (OUTLIER) cc_final: 0.4845 (mttm) REVERT: A 309 GLU cc_start: 0.5633 (pm20) cc_final: 0.5404 (pm20) REVERT: A 370 GLU cc_start: 0.7637 (mm-30) cc_final: 0.6912 (mm-30) REVERT: B 9 GLN cc_start: 0.6448 (OUTLIER) cc_final: 0.6105 (mt0) REVERT: B 12 GLU cc_start: 0.6808 (tp30) cc_final: 0.6469 (tt0) REVERT: B 19 ARG cc_start: 0.7810 (ttp-110) cc_final: 0.7259 (ttm-80) REVERT: B 197 ARG cc_start: 0.8298 (mmm-85) cc_final: 0.7766 (mmm160) REVERT: B 214 ARG cc_start: 0.7500 (mmt180) cc_final: 0.7050 (mmt180) REVERT: B 215 GLU cc_start: 0.7561 (mp0) cc_final: 0.7237 (mt-10) REVERT: B 304 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7880 (ttp-170) REVERT: E 40 CYS cc_start: 0.2548 (OUTLIER) cc_final: 0.2031 (p) REVERT: G 13 ARG cc_start: 0.6284 (ttm170) cc_final: 0.5955 (ttm110) REVERT: R 48 MET cc_start: 0.4452 (ptp) cc_final: 0.3559 (ttt) REVERT: R 90 LEU cc_start: 0.2098 (OUTLIER) cc_final: 0.1208 (pt) REVERT: R 120 LYS cc_start: 0.5229 (OUTLIER) cc_final: 0.4939 (mmtm) REVERT: R 140 GLU cc_start: 0.6263 (mm-30) cc_final: 0.5899 (mp0) REVERT: R 171 VAL cc_start: 0.7335 (t) cc_final: 0.6992 (m) REVERT: R 254 THR cc_start: 0.7118 (m) cc_final: 0.6568 (p) REVERT: R 264 LEU cc_start: 0.8005 (tp) cc_final: 0.7709 (mt) REVERT: R 328 ARG cc_start: 0.7313 (mtt180) cc_final: 0.6822 (mtt-85) REVERT: R 343 LYS cc_start: 0.8073 (tttt) cc_final: 0.7498 (tmmt) REVERT: R 364 SER cc_start: 0.8069 (m) cc_final: 0.7356 (p) REVERT: R 367 MET cc_start: 0.5307 (tmm) cc_final: 0.5094 (tmm) REVERT: R 368 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6743 (tp) outliers start: 24 outliers final: 14 residues processed: 181 average time/residue: 0.6993 time to fit residues: 134.4603 Evaluate side-chains 184 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 120 LYS Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 38 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 93 optimal weight: 0.0970 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 55 optimal weight: 0.0980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 91 HIS B 266 HIS B 340 ASN N 13 GLN R 257 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.196976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.151755 restraints weight = 15852.612| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 3.78 r_work: 0.3113 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10490 Z= 0.107 Angle : 0.546 8.980 14190 Z= 0.283 Chirality : 0.041 0.202 1558 Planarity : 0.004 0.040 1775 Dihedral : 8.156 89.405 1604 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.65 % Allowed : 16.07 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.14 (0.25), residues: 1251 helix: 2.31 (0.23), residues: 509 sheet: 0.10 (0.32), residues: 239 loop : -0.53 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.013 0.001 TYR R 191 PHE 0.013 0.001 PHE B 151 TRP 0.015 0.002 TRP A 234 HIS 0.002 0.001 HIS R 302 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (10478) covalent geometry : angle 0.54127 / 0.28 (14166) SS BOND : bond 0.00445 / 0.35 ( 9) SS BOND : angle 1.06956 / 0.70 ( 18) hydrogen bonds : bond 0.04145 / 2.75 ( 528) hydrogen bonds : angle 4.45122 / 3.15 ( 1489) Misc. bond : bond 0.00018 / 0.01 ( 1) link_NAG-ASN : bond 0.00345 / 0.18 ( 2) link_NAG-ASN : angle 2.97596 / 1.40 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5896.11 seconds wall clock time: 100 minutes 50.58 seconds (6050.58 seconds total)