Starting phenix.real_space_refine on Wed Mar 4 05:17:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyf_26178/03_2026/7tyf_26178.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyf_26178/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tyf_26178/03_2026/7tyf_26178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyf_26178/03_2026/7tyf_26178.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tyf_26178/03_2026/7tyf_26178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyf_26178/03_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-5986/lib/python3.9/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 dihedrals: 6 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: 2.11, 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: 0.88 Conformation dependent library (CDL) restraints added in 485.7 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: 0.31 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: 1.57 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 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: 6089 26.66 - 53.32: 241 53.32 - 79.98: 48 79.98 - 106.64: 4 106.64 - 133.30: 2 Dihedral angle restraints: 6384 sinusoidal: 2692 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 6381 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: 1.430 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.960 Find NCS groups from input model: 0.050 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:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 14.565 133.305 3973 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 covalent geometry : bond 0.00389 (10478) covalent geometry : angle 0.57163 (14166) SS BOND : bond 0.00351 ( 9) SS BOND : angle 0.92906 ( 18) hydrogen bonds : bond 0.22690 ( 528) hydrogen bonds : angle 7.85798 ( 1489) Misc. bond : bond 0.10594 ( 1) link_NAG-ASN : bond 0.00934 ( 2) link_NAG-ASN : angle 3.05914 ( 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 : 0.337 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: 0.7255 time to fit residues: 148.1985 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 : 0.368 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.193686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.148389 restraints weight = 15471.173| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.56 r_work: 0.3050 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1416 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= 0.168 Angle : 0.605 7.513 14190 Z= 0.328 Chirality : 0.045 0.153 1558 Planarity : 0.005 0.041 1775 Dihedral : 9.164 91.969 1794 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.61 % Allowed : 12.49 % Favored : 84.90 % 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: -0.04 (0.23), residues: 1251 helix: 1.03 (0.22), residues: 510 sheet: -0.16 (0.32), residues: 240 loop : -1.00 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 219 TYR 0.025 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 covalent geometry : bond 0.00351 (10478) covalent geometry : angle 0.60379 (14166) SS BOND : bond 0.00399 ( 9) SS BOND : angle 1.10931 ( 18) hydrogen bonds : bond 0.05648 ( 528) hydrogen bonds : angle 5.11648 ( 1489) Misc. bond : bond 0.00023 ( 1) link_NAG-ASN : bond 0.00457 ( 2) link_NAG-ASN : angle 1.47512 ( 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 207 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7108 (mtm-85) cc_final: 0.6392 (mpt180) REVERT: A 35 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7393 (mm110) REVERT: A 370 GLU cc_start: 0.7560 (mm-30) cc_final: 0.6904 (mp0) REVERT: B 19 ARG cc_start: 0.7803 (ttp-110) cc_final: 0.7224 (ttm-80) REVERT: B 44 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6637 (pt0) REVERT: B 197 ARG cc_start: 0.8340 (mmm-85) cc_final: 0.7760 (mmm160) REVERT: B 214 ARG cc_start: 0.7512 (mmt180) cc_final: 0.7039 (mmt180) REVERT: G 13 ARG cc_start: 0.6341 (ttm170) cc_final: 0.6056 (ttm110) REVERT: R 140 GLU cc_start: 0.6282 (mm-30) cc_final: 0.5798 (mp0) REVERT: R 171 VAL cc_start: 0.7410 (t) cc_final: 0.7061 (m) REVERT: R 174 ARG cc_start: 0.6423 (mtp180) cc_final: 0.6173 (mtp180) REVERT: R 258 ARG cc_start: 0.6922 (mtm180) cc_final: 0.6064 (mtt-85) REVERT: R 271 LEU cc_start: 0.7788 (mt) cc_final: 0.7573 (mt) REVERT: R 321 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7720 (ttt-90) REVERT: R 328 ARG cc_start: 0.7318 (mtt180) cc_final: 0.6833 (mtt-85) REVERT: R 343 LYS cc_start: 0.8029 (tttt) cc_final: 0.7427 (tmmt) outliers start: 27 outliers final: 13 residues processed: 194 average time/residue: 0.7038 time to fit residues: 144.8069 Evaluate side-chains 181 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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: 0.0670 chunk 25 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN E 140 GLN N 3 GLN N 13 GLN N 77 ASN R 257 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.193868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.160497 restraints weight = 13935.268| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.15 r_work: 0.3071 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 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 = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10490 Z= 0.149 Angle : 0.573 7.497 14190 Z= 0.308 Chirality : 0.044 0.162 1558 Planarity : 0.004 0.041 1775 Dihedral : 8.486 74.083 1788 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.61 % Allowed : 12.78 % Favored : 84.61 % 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: 0.44 (0.23), residues: 1251 helix: 1.52 (0.23), residues: 515 sheet: -0.03 (0.32), residues: 237 loop : -0.81 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.019 0.002 TYR R 56 PHE 0.013 0.001 PHE B 151 TRP 0.021 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00309 (10478) covalent geometry : angle 0.57208 (14166) SS BOND : bond 0.00385 ( 9) SS BOND : angle 0.95816 ( 18) hydrogen bonds : bond 0.05311 ( 528) hydrogen bonds : angle 4.89127 ( 1489) Misc. bond : bond 0.00027 ( 1) link_NAG-ASN : bond 0.00331 ( 2) link_NAG-ASN : angle 1.05453 ( 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 201 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7112 (mtm-85) cc_final: 0.6529 (mpt180) REVERT: A 35 GLN cc_start: 0.7694 (tm-30) cc_final: 0.7440 (mm110) REVERT: A 296 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6751 (mp) REVERT: A 370 GLU cc_start: 0.7626 (mm-30) cc_final: 0.6870 (OUTLIER) REVERT: B 12 GLU cc_start: 0.7016 (tp30) cc_final: 0.6626 (tt0) REVERT: B 19 ARG cc_start: 0.7912 (ttp-110) cc_final: 0.7407 (ttm-80) REVERT: B 44 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6570 (pt0) REVERT: B 197 ARG cc_start: 0.8331 (mmm-85) cc_final: 0.7804 (mmm160) REVERT: B 214 ARG cc_start: 0.7469 (mmt180) cc_final: 0.7049 (mmt180) REVERT: B 215 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: G 38 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8335 (ptt) REVERT: R 140 GLU cc_start: 0.6262 (mm-30) cc_final: 0.5920 (mp0) REVERT: R 171 VAL cc_start: 0.7450 (t) cc_final: 0.7135 (m) REVERT: R 258 ARG cc_start: 0.6976 (mtm180) cc_final: 0.6056 (mtt-85) REVERT: R 328 ARG cc_start: 0.7314 (mtt180) cc_final: 0.6826 (mtt-85) REVERT: R 343 LYS cc_start: 0.8111 (tttt) cc_final: 0.7556 (tmmt) REVERT: R 364 SER cc_start: 0.8113 (m) cc_final: 0.7361 (p) outliers start: 27 outliers final: 16 residues processed: 186 average time/residue: 0.6959 time to fit residues: 137.2613 Evaluate side-chains 187 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 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 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 B residue 215 GLU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 38 MET 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: 10.0000 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN E 140 GLN N 3 GLN N 13 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 = 0.194617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.150778 restraints weight = 14847.886| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.41 r_work: 0.3068 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10490 Z= 0.134 Angle : 0.550 7.711 14190 Z= 0.294 Chirality : 0.043 0.172 1558 Planarity : 0.004 0.041 1775 Dihedral : 8.236 75.435 1787 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.90 % Allowed : 13.17 % 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: 0.68 (0.24), residues: 1251 helix: 1.80 (0.23), residues: 515 sheet: -0.03 (0.32), residues: 237 loop : -0.71 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 98 TYR 0.019 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 covalent geometry : bond 0.00274 (10478) covalent geometry : angle 0.54859 (14166) SS BOND : bond 0.00342 ( 9) SS BOND : angle 0.99103 ( 18) hydrogen bonds : bond 0.04854 ( 528) hydrogen bonds : angle 4.70288 ( 1489) Misc. bond : bond 0.00022 ( 1) link_NAG-ASN : bond 0.00302 ( 2) link_NAG-ASN : angle 1.26454 ( 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 201 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7064 (mtm-85) cc_final: 0.6414 (mpt180) REVERT: A 27 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7709 (tp30) REVERT: A 35 GLN cc_start: 0.7645 (tm-30) cc_final: 0.7328 (mm110) REVERT: A 296 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6434 (mp) REVERT: A 370 GLU cc_start: 0.7542 (mm-30) cc_final: 0.6727 (OUTLIER) REVERT: B 12 GLU cc_start: 0.6907 (tp30) cc_final: 0.6418 (tt0) REVERT: B 19 ARG cc_start: 0.7779 (ttp-110) cc_final: 0.7164 (ttm-80) REVERT: B 44 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6621 (pt0) REVERT: B 197 ARG cc_start: 0.8355 (mmm-85) cc_final: 0.7780 (mmm160) REVERT: B 214 ARG cc_start: 0.7496 (mmt180) cc_final: 0.7065 (mmt180) REVERT: B 304 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7910 (ttp-170) REVERT: E 40 CYS cc_start: 0.2651 (OUTLIER) cc_final: 0.2046 (p) REVERT: G 38 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8271 (ptt) REVERT: R 140 GLU cc_start: 0.6029 (mm-30) cc_final: 0.5616 (mp0) REVERT: R 171 VAL cc_start: 0.7270 (t) cc_final: 0.6913 (m) REVERT: R 174 ARG cc_start: 0.6433 (mtp180) cc_final: 0.6063 (mtp180) REVERT: R 254 THR cc_start: 0.6972 (m) cc_final: 0.6443 (p) REVERT: R 264 LEU cc_start: 0.7981 (tp) cc_final: 0.7638 (mt) REVERT: R 328 ARG cc_start: 0.7221 (mtt180) cc_final: 0.6719 (mtt-85) REVERT: R 343 LYS cc_start: 0.8018 (tttt) cc_final: 0.7396 (tmmt) REVERT: R 364 SER cc_start: 0.8030 (m) cc_final: 0.7267 (p) outliers start: 30 outliers final: 16 residues processed: 186 average time/residue: 0.7263 time to fit residues: 143.2763 Evaluate side-chains 186 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 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 G residue 38 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 73 optimal weight: 20.0000 chunk 60 optimal weight: 0.0040 chunk 82 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 39 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 91 HIS N 3 GLN R 208 ASN R 257 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.197797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.159946 restraints weight = 17524.054| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.70 r_work: 0.3128 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 : 0.002 0.028 10490 Z= 0.100 Angle : 0.497 8.024 14190 Z= 0.262 Chirality : 0.041 0.178 1558 Planarity : 0.003 0.042 1775 Dihedral : 7.663 76.117 1787 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.03 % Allowed : 14.91 % Favored : 83.06 % 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: 1.03 (0.24), residues: 1251 helix: 2.23 (0.23), residues: 509 sheet: -0.01 (0.32), residues: 237 loop : -0.56 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.020 0.001 TYR R 56 PHE 0.011 0.001 PHE R 269 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00199 (10478) covalent geometry : angle 0.49593 (14166) SS BOND : bond 0.00225 ( 9) SS BOND : angle 0.81422 ( 18) hydrogen bonds : bond 0.04065 ( 528) hydrogen bonds : angle 4.40320 ( 1489) Misc. bond : bond 0.00012 ( 1) link_NAG-ASN : bond 0.00253 ( 2) link_NAG-ASN : angle 1.08526 ( 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 205 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7079 (mtm-85) cc_final: 0.6503 (mpt180) REVERT: A 27 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7762 (tp30) REVERT: A 35 GLN cc_start: 0.7703 (tm-30) cc_final: 0.7332 (mm110) REVERT: A 370 GLU cc_start: 0.7549 (mm-30) cc_final: 0.6789 (tp30) REVERT: B 12 GLU cc_start: 0.7018 (tp30) cc_final: 0.6622 (tt0) REVERT: B 15 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7286 (mtpm) REVERT: B 19 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7324 (ttm-80) REVERT: B 44 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6570 (pt0) REVERT: B 46 ARG cc_start: 0.7856 (mmm160) cc_final: 0.7638 (tpp-160) REVERT: B 197 ARG cc_start: 0.8342 (mmm-85) cc_final: 0.7817 (mmm160) REVERT: B 214 ARG cc_start: 0.7446 (mmt180) cc_final: 0.7027 (mmt180) REVERT: B 304 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7876 (ttp-170) REVERT: E 40 CYS cc_start: 0.2612 (OUTLIER) cc_final: 0.2184 (p) REVERT: G 13 ARG cc_start: 0.6335 (ttm170) cc_final: 0.5976 (ttm110) REVERT: R 130 ASN cc_start: 0.3485 (OUTLIER) cc_final: 0.2807 (t0) REVERT: R 140 GLU cc_start: 0.6062 (mm-30) cc_final: 0.5680 (mp0) REVERT: R 171 VAL cc_start: 0.7318 (t) cc_final: 0.6942 (m) REVERT: R 174 ARG cc_start: 0.6515 (mtp180) cc_final: 0.6135 (mtp180) REVERT: R 208 ASN cc_start: 0.6248 (OUTLIER) cc_final: 0.6035 (t0) REVERT: R 254 THR cc_start: 0.7033 (m) cc_final: 0.6523 (p) REVERT: R 264 LEU cc_start: 0.7955 (tp) cc_final: 0.7637 (mt) REVERT: R 328 ARG cc_start: 0.7209 (mtt180) cc_final: 0.6739 (mtt-85) REVERT: R 343 LYS cc_start: 0.8083 (tttt) cc_final: 0.7497 (tmmt) REVERT: R 367 MET cc_start: 0.5288 (tmm) cc_final: 0.5052 (tmm) outliers start: 21 outliers final: 6 residues processed: 195 average time/residue: 0.7209 time to fit residues: 149.0432 Evaluate side-chains 181 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 168 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 B residue 15 LYS 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 304 ARG Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain R residue 208 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 35 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 32 GLN B 266 HIS B 340 ASN E 140 GLN N 13 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 = 0.4097 r_free = 0.4097 target = 0.193164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.130565 restraints weight = 10852.930| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.76 r_work: 0.3184 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 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 = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1900 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= 0.179 Angle : 0.611 8.175 14190 Z= 0.326 Chirality : 0.045 0.187 1558 Planarity : 0.004 0.042 1775 Dihedral : 8.575 76.257 1787 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.42 % Allowed : 15.10 % Favored : 82.48 % 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: 0.80 (0.24), residues: 1251 helix: 1.92 (0.23), residues: 515 sheet: -0.08 (0.32), residues: 240 loop : -0.61 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 347 TYR 0.014 0.002 TYR P 37 PHE 0.015 0.002 PHE R 269 TRP 0.023 0.002 TRP A 234 HIS 0.007 0.002 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00378 (10478) covalent geometry : angle 0.60881 (14166) SS BOND : bond 0.00483 ( 9) SS BOND : angle 1.24856 ( 18) hydrogen bonds : bond 0.05352 ( 528) hydrogen bonds : angle 4.79662 ( 1489) Misc. bond : bond 0.00034 ( 1) link_NAG-ASN : bond 0.00407 ( 2) link_NAG-ASN : angle 1.60314 ( 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 190 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7834 (tp30) REVERT: A 296 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6694 (mp) REVERT: A 370 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6744 (OUTLIER) REVERT: B 9 GLN cc_start: 0.6613 (OUTLIER) cc_final: 0.6215 (mt0) REVERT: B 12 GLU cc_start: 0.6962 (tp30) cc_final: 0.6555 (tt0) REVERT: B 19 ARG cc_start: 0.7789 (ttp-110) cc_final: 0.7194 (ttm-80) REVERT: B 44 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6625 (pt0) REVERT: B 197 ARG cc_start: 0.8329 (mmm-85) cc_final: 0.7810 (mmm160) REVERT: E 40 CYS cc_start: 0.2537 (OUTLIER) cc_final: 0.1991 (p) REVERT: G 13 ARG cc_start: 0.6376 (ttm170) cc_final: 0.6054 (ttm110) REVERT: G 46 LYS cc_start: 0.7860 (mttt) cc_final: 0.7628 (mmtm) REVERT: R 48 MET cc_start: 0.4356 (ptp) cc_final: 0.3328 (ttt) REVERT: R 140 GLU cc_start: 0.6121 (mm-30) cc_final: 0.5718 (mp0) REVERT: R 171 VAL cc_start: 0.7302 (t) cc_final: 0.6965 (m) REVERT: R 174 ARG cc_start: 0.6538 (mtp180) cc_final: 0.6185 (mtp180) REVERT: R 208 ASN cc_start: 0.5942 (OUTLIER) cc_final: 0.5410 (p0) REVERT: R 254 THR cc_start: 0.7097 (m) cc_final: 0.6518 (p) REVERT: R 264 LEU cc_start: 0.7968 (tp) cc_final: 0.7649 (mt) REVERT: R 328 ARG cc_start: 0.7229 (mtt180) cc_final: 0.6697 (mtt-85) REVERT: R 343 LYS cc_start: 0.7998 (tttt) cc_final: 0.7383 (tmmt) REVERT: R 364 SER cc_start: 0.8077 (OUTLIER) cc_final: 0.7276 (p) REVERT: R 367 MET cc_start: 0.5383 (tmm) cc_final: 0.5059 (tmm) outliers start: 25 outliers final: 16 residues processed: 182 average time/residue: 0.7527 time to fit residues: 145.1574 Evaluate side-chains 184 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 365 CYS Chi-restraints excluded: chain A residue 367 VAL 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 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 208 ASN 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 364 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 37 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 266 HIS B 340 ASN E 140 GLN N 13 GLN R 208 ASN R 257 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.194836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.149424 restraints weight = 15731.058| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.78 r_work: 0.3077 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10490 Z= 0.126 Angle : 0.547 8.718 14190 Z= 0.290 Chirality : 0.042 0.189 1558 Planarity : 0.004 0.042 1775 Dihedral : 8.238 76.663 1785 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.03 % Allowed : 15.78 % Favored : 82.19 % 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: 0.95 (0.24), residues: 1251 helix: 2.12 (0.23), residues: 515 sheet: -0.01 (0.32), residues: 237 loop : -0.61 (0.28), residues: 499 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 0.013 0.001 PHE B 151 TRP 0.020 0.002 TRP A 234 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00258 (10478) covalent geometry : angle 0.54577 (14166) SS BOND : bond 0.00322 ( 9) SS BOND : angle 0.96473 ( 18) hydrogen bonds : bond 0.04656 ( 528) hydrogen bonds : angle 4.59451 ( 1489) Misc. bond : bond 0.00025 ( 1) link_NAG-ASN : bond 0.00316 ( 2) link_NAG-ASN : angle 1.28772 ( 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 188 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7761 (tp30) REVERT: A 35 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7293 (mm110) REVERT: A 300 LYS cc_start: 0.5276 (OUTLIER) cc_final: 0.4909 (mttm) REVERT: A 370 GLU cc_start: 0.7542 (mm-30) cc_final: 0.6811 (mm-30) REVERT: B 9 GLN cc_start: 0.6528 (OUTLIER) cc_final: 0.6121 (mt0) REVERT: B 12 GLU cc_start: 0.6919 (tp30) cc_final: 0.6508 (tt0) REVERT: B 19 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7193 (ttm-80) REVERT: B 44 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6581 (pt0) REVERT: B 197 ARG cc_start: 0.8328 (mmm-85) cc_final: 0.7600 (mmm160) REVERT: B 212 ASP cc_start: 0.8704 (t70) cc_final: 0.8482 (t70) REVERT: B 304 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7908 (ttp-170) REVERT: E 40 CYS cc_start: 0.2565 (OUTLIER) cc_final: 0.2007 (p) REVERT: G 13 ARG cc_start: 0.6232 (ttm170) cc_final: 0.5870 (ttm110) REVERT: G 46 LYS cc_start: 0.7839 (mttt) cc_final: 0.7591 (mmtm) REVERT: R 48 MET cc_start: 0.4286 (ptp) cc_final: 0.3321 (ttt) REVERT: R 120 LYS cc_start: 0.5345 (OUTLIER) cc_final: 0.5021 (mmtm) REVERT: R 140 GLU cc_start: 0.6045 (mm-30) cc_final: 0.5665 (mp0) REVERT: R 171 VAL cc_start: 0.7260 (t) cc_final: 0.6897 (m) REVERT: R 174 ARG cc_start: 0.6550 (mtp180) cc_final: 0.6238 (mtp180) REVERT: R 254 THR cc_start: 0.6986 (m) cc_final: 0.6478 (p) REVERT: R 264 LEU cc_start: 0.7958 (tp) cc_final: 0.7642 (mt) REVERT: R 328 ARG cc_start: 0.7206 (mtt180) cc_final: 0.6697 (mtt-85) REVERT: R 343 LYS cc_start: 0.8021 (tttt) cc_final: 0.7395 (tmmt) REVERT: R 364 SER cc_start: 0.8044 (OUTLIER) cc_final: 0.7249 (p) REVERT: R 367 MET cc_start: 0.5317 (tmm) cc_final: 0.5093 (tmm) outliers start: 21 outliers final: 12 residues processed: 182 average time/residue: 0.7857 time to fit residues: 151.0697 Evaluate side-chains 183 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 300 LYS Chi-restraints excluded: chain A residue 367 VAL 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 120 LYS Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 364 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 85 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 24 optimal weight: 0.0770 chunk 60 optimal weight: 0.0020 chunk 104 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 overall best weight: 0.4346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 266 HIS B 340 ASN N 13 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 = 0.4147 r_free = 0.4147 target = 0.198185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.151210 restraints weight = 18111.887| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 4.26 r_work: 0.3135 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10490 Z= 0.101 Angle : 0.566 22.577 14190 Z= 0.277 Chirality : 0.046 0.864 1558 Planarity : 0.003 0.041 1775 Dihedral : 8.117 76.365 1785 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.84 % Allowed : 15.97 % Favored : 82.19 % 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: 1.27 (0.25), residues: 1251 helix: 2.49 (0.23), residues: 509 sheet: 0.12 (0.32), residues: 241 loop : -0.52 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 347 TYR 0.013 0.001 TYR R 131 PHE 0.012 0.001 PHE B 151 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS R 381 Details of bonding type rmsd covalent geometry : bond 0.00201 (10478) covalent geometry : angle 0.52013 (14166) SS BOND : bond 0.00214 ( 9) SS BOND : angle 0.78434 ( 18) hydrogen bonds : bond 0.03941 ( 528) hydrogen bonds : angle 4.32260 ( 1489) Misc. bond : bond 0.00029 ( 1) link_NAG-ASN : bond 0.01405 ( 2) link_NAG-ASN : angle 10.76104 ( 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 196 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7124 (mtm-85) cc_final: 0.6514 (mpt180) REVERT: A 27 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7670 (tp30) REVERT: A 35 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7217 (mm110) REVERT: A 370 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6754 (mm-30) REVERT: B 9 GLN cc_start: 0.6449 (OUTLIER) cc_final: 0.6044 (mt0) REVERT: B 12 GLU cc_start: 0.6759 (tp30) cc_final: 0.6367 (tt0) REVERT: B 19 ARG cc_start: 0.7753 (ttp-110) cc_final: 0.7193 (ttm-80) REVERT: B 155 ASN cc_start: 0.8167 (t0) cc_final: 0.7928 (t0) REVERT: B 197 ARG cc_start: 0.8314 (mmm-85) cc_final: 0.7594 (mmm160) REVERT: B 212 ASP cc_start: 0.8542 (t70) cc_final: 0.8308 (t70) REVERT: B 215 GLU cc_start: 0.7761 (mp0) cc_final: 0.7085 (mt-10) REVERT: B 304 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7846 (ttp-170) REVERT: E 40 CYS cc_start: 0.2475 (OUTLIER) cc_final: 0.1895 (p) REVERT: G 13 ARG cc_start: 0.6145 (ttm170) cc_final: 0.5782 (ttm110) REVERT: R 48 MET cc_start: 0.4145 (ptp) cc_final: 0.3296 (ttt) REVERT: R 140 GLU cc_start: 0.5967 (mm-30) cc_final: 0.5535 (mp0) REVERT: R 171 VAL cc_start: 0.7151 (t) cc_final: 0.6762 (m) REVERT: R 174 ARG cc_start: 0.6555 (mtp180) cc_final: 0.6305 (mtp180) REVERT: R 254 THR cc_start: 0.6988 (m) cc_final: 0.6478 (p) REVERT: R 264 LEU cc_start: 0.7899 (tp) cc_final: 0.7589 (mt) REVERT: R 328 ARG cc_start: 0.7132 (mtt180) cc_final: 0.6641 (mtt-85) REVERT: R 343 LYS cc_start: 0.7997 (tttt) cc_final: 0.7393 (tmmt) REVERT: R 367 MET cc_start: 0.5246 (tmm) cc_final: 0.5013 (tmm) outliers start: 19 outliers final: 10 residues processed: 190 average time/residue: 0.7193 time to fit residues: 144.6657 Evaluate side-chains 183 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 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 R residue 120 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4107 r_free = 0.4107 target = 0.194267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.145011 restraints weight = 13112.613| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.30 r_work: 0.3224 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10490 Z= 0.150 Angle : 0.618 20.223 14190 Z= 0.316 Chirality : 0.047 0.731 1558 Planarity : 0.004 0.043 1775 Dihedral : 8.625 77.307 1785 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.03 % Allowed : 16.07 % Favored : 81.90 % 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: 1.07 (0.24), residues: 1251 helix: 2.22 (0.23), residues: 515 sheet: 0.11 (0.32), residues: 241 loop : -0.59 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 283 TYR 0.013 0.002 TYR R 56 PHE 0.014 0.001 PHE R 269 TRP 0.022 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00313 (10478) covalent geometry : angle 0.58483 (14166) SS BOND : bond 0.00428 ( 9) SS BOND : angle 1.20329 ( 18) hydrogen bonds : bond 0.04921 ( 528) hydrogen bonds : angle 4.63256 ( 1489) Misc. bond : bond 0.00035 ( 1) link_NAG-ASN : bond 0.01160 ( 2) link_NAG-ASN : angle 9.54840 ( 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 187 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7910 (tp30) REVERT: A 300 LYS cc_start: 0.5498 (OUTLIER) cc_final: 0.5121 (mttm) REVERT: A 370 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6839 (mm-30) REVERT: B 9 GLN cc_start: 0.6549 (OUTLIER) cc_final: 0.6141 (mt0) REVERT: B 12 GLU cc_start: 0.6899 (tp30) cc_final: 0.6541 (tt0) REVERT: B 19 ARG cc_start: 0.7807 (ttp-110) cc_final: 0.7283 (ttm-80) REVERT: B 197 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.7789 (mmm160) REVERT: B 212 ASP cc_start: 0.8648 (t70) cc_final: 0.8447 (t70) REVERT: B 215 GLU cc_start: 0.7623 (mp0) cc_final: 0.7029 (mt-10) REVERT: B 304 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7871 (ttp-170) REVERT: E 40 CYS cc_start: 0.2495 (OUTLIER) cc_final: 0.1935 (p) REVERT: G 13 ARG cc_start: 0.6248 (ttm170) cc_final: 0.5904 (ttm110) REVERT: R 48 MET cc_start: 0.4236 (ptp) cc_final: 0.3350 (ttt) REVERT: R 120 LYS cc_start: 0.5370 (OUTLIER) cc_final: 0.5050 (mmtm) REVERT: R 140 GLU cc_start: 0.5987 (mm-30) cc_final: 0.5629 (mp0) REVERT: R 171 VAL cc_start: 0.7246 (t) cc_final: 0.6891 (m) REVERT: R 174 ARG cc_start: 0.6558 (mtp180) cc_final: 0.6262 (mtp180) REVERT: R 254 THR cc_start: 0.7118 (m) cc_final: 0.6577 (p) REVERT: R 264 LEU cc_start: 0.7936 (tp) cc_final: 0.7646 (mt) REVERT: R 328 ARG cc_start: 0.7247 (mtt180) cc_final: 0.6777 (mtt-85) REVERT: R 343 LYS cc_start: 0.8055 (tttt) cc_final: 0.7475 (tmmt) REVERT: R 367 MET cc_start: 0.5334 (tmm) cc_final: 0.5033 (tmm) REVERT: R 368 LEU cc_start: 0.7050 (mt) cc_final: 0.6740 (tp) outliers start: 21 outliers final: 12 residues processed: 181 average time/residue: 0.7580 time to fit residues: 144.8070 Evaluate side-chains 182 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 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 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 120 LYS Chi-restraints excluded: chain R residue 364 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 104 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 266 HIS B 340 ASN N 13 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 = 0.4109 r_free = 0.4109 target = 0.194530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.130807 restraints weight = 13284.788| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.99 r_work: 0.3168 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 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 = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10490 Z= 0.143 Angle : 0.609 18.696 14190 Z= 0.313 Chirality : 0.046 0.630 1558 Planarity : 0.004 0.043 1775 Dihedral : 8.725 77.922 1785 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.84 % Allowed : 16.55 % Favored : 81.61 % 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: 1.04 (0.24), residues: 1251 helix: 2.19 (0.23), residues: 515 sheet: 0.09 (0.32), residues: 241 loop : -0.60 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 283 TYR 0.016 0.002 TYR R 56 PHE 0.014 0.001 PHE R 269 TRP 0.021 0.002 TRP A 234 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00297 (10478) covalent geometry : angle 0.58167 (14166) SS BOND : bond 0.00441 ( 9) SS BOND : angle 1.07775 ( 18) hydrogen bonds : bond 0.04801 ( 528) hydrogen bonds : angle 4.62228 ( 1489) Misc. bond : bond 0.00031 ( 1) link_NAG-ASN : bond 0.01178 ( 2) link_NAG-ASN : angle 8.70798 ( 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 189 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7930 (tp30) REVERT: A 35 GLN cc_start: 0.7667 (tm-30) cc_final: 0.7331 (mm110) REVERT: A 296 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6667 (mp) REVERT: A 300 LYS cc_start: 0.5446 (OUTLIER) cc_final: 0.5074 (mttm) REVERT: A 370 GLU cc_start: 0.7586 (mm-30) cc_final: 0.6851 (mm-30) REVERT: B 9 GLN cc_start: 0.6518 (OUTLIER) cc_final: 0.6131 (mt0) REVERT: B 12 GLU cc_start: 0.7007 (tp30) cc_final: 0.6580 (tt0) REVERT: B 19 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7196 (ttm-80) REVERT: B 197 ARG cc_start: 0.8388 (mmm-85) cc_final: 0.7635 (mmm160) REVERT: B 212 ASP cc_start: 0.8674 (t70) cc_final: 0.8400 (t70) REVERT: B 215 GLU cc_start: 0.7639 (mp0) cc_final: 0.6941 (mt-10) REVERT: B 304 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7931 (ttp-170) REVERT: B 340 ASN cc_start: 0.7727 (t0) cc_final: 0.7523 (t160) REVERT: E 40 CYS cc_start: 0.2479 (OUTLIER) cc_final: 0.1869 (p) REVERT: G 13 ARG cc_start: 0.6325 (ttm170) cc_final: 0.5972 (ttm110) REVERT: G 46 LYS cc_start: 0.7877 (mttt) cc_final: 0.7621 (mmtm) REVERT: R 48 MET cc_start: 0.4202 (ptp) cc_final: 0.3276 (ttt) REVERT: R 120 LYS cc_start: 0.5311 (OUTLIER) cc_final: 0.5002 (mmtm) REVERT: R 140 GLU cc_start: 0.6184 (mm-30) cc_final: 0.5726 (mp0) REVERT: R 171 VAL cc_start: 0.7217 (t) cc_final: 0.6848 (m) REVERT: R 174 ARG cc_start: 0.6503 (mtp180) cc_final: 0.6245 (mtp180) REVERT: R 254 THR cc_start: 0.7071 (m) cc_final: 0.6543 (p) REVERT: R 264 LEU cc_start: 0.7979 (tp) cc_final: 0.7675 (mt) REVERT: R 328 ARG cc_start: 0.7209 (mtt180) cc_final: 0.6735 (mtt-85) REVERT: R 343 LYS cc_start: 0.8048 (tttt) cc_final: 0.7427 (tmmt) REVERT: R 364 SER cc_start: 0.7997 (OUTLIER) cc_final: 0.7237 (p) REVERT: R 367 MET cc_start: 0.5380 (tmm) cc_final: 0.5091 (tmm) REVERT: R 368 LEU cc_start: 0.7044 (mt) cc_final: 0.6741 (tp) outliers start: 19 outliers final: 11 residues processed: 184 average time/residue: 0.7399 time to fit residues: 143.8756 Evaluate side-chains 183 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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 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 120 LYS Chi-restraints excluded: chain R residue 364 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 38 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 40 optimal weight: 0.0370 chunk 65 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 266 HIS E 140 GLN N 13 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 = 0.4086 r_free = 0.4086 target = 0.192143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.146256 restraints weight = 15422.660| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.63 r_work: 0.3039 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10490 Z= 0.224 Angle : 0.717 17.788 14190 Z= 0.374 Chirality : 0.051 0.620 1558 Planarity : 0.005 0.043 1775 Dihedral : 10.075 86.193 1785 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.23 % Allowed : 16.26 % Favored : 81.51 % 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: 0.71 (0.24), residues: 1251 helix: 1.83 (0.23), residues: 509 sheet: 0.00 (0.32), residues: 244 loop : -0.67 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 58 TYR 0.017 0.002 TYR R 284 PHE 0.019 0.002 PHE R 269 TRP 0.024 0.002 TRP A 234 HIS 0.008 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00479 (10478) covalent geometry : angle 0.69537 (14166) SS BOND : bond 0.00698 ( 9) SS BOND : angle 1.44301 ( 18) hydrogen bonds : bond 0.05869 ( 528) hydrogen bonds : angle 4.94479 ( 1489) Misc. bond : bond 0.00033 ( 1) link_NAG-ASN : bond 0.01114 ( 2) link_NAG-ASN : angle 8.20358 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6172.30 seconds wall clock time: 105 minutes 21.67 seconds (6321.67 seconds total)