Starting phenix.real_space_refine on Sun Dec 29 18:18:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyf_26178/12_2024/7tyf_26178.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyf_26178/12_2024/7tyf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyf_26178/12_2024/7tyf_26178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyf_26178/12_2024/7tyf_26178.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyf_26178/12_2024/7tyf_26178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyf_26178/12_2024/7tyf_26178.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} 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: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} 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: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 3} 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: 7.38, per 1000 atoms: 0.71 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: 2.96 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.04 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: 2.85 Time building geometry restraints manager: 3.20 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: 1.130 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.780 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.980 ------------------------------------------------------------------------------- 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 0.050 10478 Z= 0.254 Angle : 0.572 9.523 14166 Z= 0.324 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (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 TRP 0.016 0.001 TRP A 234 HIS 0.005 0.001 HIS A 41 PHE 0.012 0.001 PHE B 151 TYR 0.009 0.001 TYR R 65 ARG 0.004 0.000 ARG R 213 *********************** 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 : 1.134 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: 0.7326 (mmm160) REVERT: B 214 ARG cc_start: 0.7199 (mmt180) cc_final: 0.6854 (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: 1.5506 time to fit residues: 317.7556 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 : 1.134 ------------------------------------------------------------------------------- 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 103 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 32 GLN B 75 GLN B 88 ASN B 155 ASN N 3 GLN N 13 GLN N 77 ASN P 22 ASN R 201 HIS R 318 ASN R 365 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10478 Z= 0.206 Angle : 0.576 7.552 14166 Z= 0.313 Chirality : 0.044 0.148 1558 Planarity : 0.004 0.041 1775 Dihedral : 9.097 99.839 1794 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.42 % Allowed : 12.78 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.23), residues: 1251 helix: 0.97 (0.22), residues: 516 sheet: -0.17 (0.32), residues: 239 loop : -0.99 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 PHE 0.013 0.001 PHE B 151 TYR 0.022 0.002 TYR R 56 ARG 0.005 0.001 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2502 Ramachandran restraints generated. 1251 Oldfield, 0 Emsley, 1251 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7533 (tp40) cc_final: 0.7323 (tp40) REVERT: A 370 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6497 (mp0) REVERT: B 16 ASN cc_start: 0.7428 (m-40) cc_final: 0.7192 (m110) REVERT: B 19 ARG cc_start: 0.7453 (ttp-110) cc_final: 0.7201 (ttm-80) REVERT: B 44 GLN cc_start: 0.6742 (OUTLIER) cc_final: 0.6219 (pt0) REVERT: B 197 ARG cc_start: 0.7620 (mmm-85) cc_final: 0.7318 (mmm160) REVERT: B 214 ARG cc_start: 0.7173 (mmt180) cc_final: 0.6813 (mmt180) REVERT: R 258 ARG cc_start: 0.6599 (mtm180) cc_final: 0.5947 (mtt-85) REVERT: R 328 ARG cc_start: 0.7030 (mtt180) cc_final: 0.6592 (mtt-85) REVERT: R 343 LYS cc_start: 0.7793 (tttt) cc_final: 0.7417 (tmmt) outliers start: 25 outliers final: 12 residues processed: 197 average time/residue: 1.5555 time to fit residues: 325.5639 Evaluate side-chains 182 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 61 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 0.2980 chunk 119 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS E 140 GLN N 3 GLN N 13 GLN N 77 ASN R 201 HIS R 257 GLN R 365 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10478 Z= 0.150 Angle : 0.521 7.677 14166 Z= 0.280 Chirality : 0.042 0.161 1558 Planarity : 0.004 0.041 1775 Dihedral : 8.037 74.709 1787 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.23 % Allowed : 13.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1251 helix: 1.74 (0.23), residues: 515 sheet: -0.07 (0.32), residues: 237 loop : -0.73 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 234 HIS 0.003 0.001 HIS R 381 PHE 0.013 0.001 PHE R 161 TYR 0.021 0.001 TYR R 56 ARG 0.003 0.000 ARG B 219 *********************** 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 199 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7143 (mp) REVERT: A 370 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6465 (mp0) REVERT: B 15 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7212 (mtpm) REVERT: B 16 ASN cc_start: 0.7441 (m-40) cc_final: 0.7170 (m110) REVERT: B 19 ARG cc_start: 0.7432 (ttp-110) cc_final: 0.7164 (ttm-80) REVERT: B 44 GLN cc_start: 0.6692 (OUTLIER) cc_final: 0.6206 (pt0) REVERT: B 197 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.7295 (mmm160) REVERT: B 214 ARG cc_start: 0.7149 (mmt180) cc_final: 0.6810 (mmt180) REVERT: R 254 THR cc_start: 0.6907 (m) cc_final: 0.6452 (p) REVERT: R 328 ARG cc_start: 0.6931 (mtt180) cc_final: 0.6488 (mtt-85) REVERT: R 343 LYS cc_start: 0.7797 (tttt) cc_final: 0.7421 (tmmt) outliers start: 23 outliers final: 10 residues processed: 187 average time/residue: 1.4793 time to fit residues: 294.3261 Evaluate side-chains 184 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 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 207 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain R residue 211 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 32 GLN B 266 HIS B 340 ASN E 140 GLN N 3 GLN N 13 GLN R 257 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10478 Z= 0.270 Angle : 0.648 7.924 14166 Z= 0.346 Chirality : 0.054 1.040 1558 Planarity : 0.005 0.042 1775 Dihedral : 8.971 74.785 1785 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.90 % Allowed : 13.75 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.24), residues: 1251 helix: 1.57 (0.23), residues: 515 sheet: -0.11 (0.32), residues: 240 loop : -0.69 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 234 HIS 0.008 0.002 HIS A 41 PHE 0.016 0.002 PHE R 269 TYR 0.021 0.002 TYR R 56 ARG 0.010 0.001 ARG A 347 *********************** 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 196 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 1.031 Fit side-chains REVERT: A 296 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7194 (mp) REVERT: A 370 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6623 (tp30) REVERT: B 16 ASN cc_start: 0.7345 (m-40) cc_final: 0.7132 (m110) REVERT: B 19 ARG cc_start: 0.7484 (ttp-110) cc_final: 0.7177 (ttm-80) REVERT: B 44 GLN cc_start: 0.6731 (OUTLIER) cc_final: 0.6247 (pt0) REVERT: B 197 ARG cc_start: 0.7584 (mmm-85) cc_final: 0.7316 (mmm160) REVERT: B 214 ARG cc_start: 0.7224 (mmt180) cc_final: 0.6786 (mmt180) REVERT: B 215 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: B 304 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7370 (ttp-170) REVERT: G 20 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7458 (mttp) REVERT: R 264 LEU cc_start: 0.7636 (tp) cc_final: 0.7381 (mt) REVERT: R 328 ARG cc_start: 0.7114 (mtt180) cc_final: 0.6628 (mtt-85) REVERT: R 343 LYS cc_start: 0.7806 (tttt) cc_final: 0.7421 (tmmt) REVERT: R 364 SER cc_start: 0.8115 (m) cc_final: 0.7393 (p) REVERT: R 367 MET cc_start: 0.5323 (tmm) cc_final: 0.5041 (tmm) outliers start: 30 outliers final: 15 residues processed: 182 average time/residue: 1.6386 time to fit residues: 317.2849 Evaluate side-chains 184 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 18 ILE 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 B residue 304 ARG Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 20 LYS 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 211 LEU Chi-restraints excluded: chain R residue 347 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 0.1980 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS B 340 ASN N 3 GLN R 257 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10478 Z= 0.220 Angle : 0.599 8.159 14166 Z= 0.319 Chirality : 0.049 0.779 1558 Planarity : 0.004 0.041 1775 Dihedral : 8.893 75.946 1785 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.10 % Allowed : 13.94 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.24), residues: 1251 helix: 1.70 (0.23), residues: 515 sheet: -0.08 (0.32), residues: 239 loop : -0.72 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 234 HIS 0.006 0.001 HIS A 41 PHE 0.014 0.001 PHE B 151 TYR 0.013 0.002 TYR P 37 ARG 0.003 0.000 ARG A 42 *********************** 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 200 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7169 (mp) REVERT: A 300 LYS cc_start: 0.6089 (OUTLIER) cc_final: 0.5641 (mttm) REVERT: A 370 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6474 (mm-30) REVERT: B 15 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7212 (mtpm) REVERT: B 16 ASN cc_start: 0.7392 (m-40) cc_final: 0.7170 (m110) REVERT: B 19 ARG cc_start: 0.7439 (ttp-110) cc_final: 0.7134 (ttm-80) REVERT: B 44 GLN cc_start: 0.6714 (OUTLIER) cc_final: 0.6204 (pt0) REVERT: B 197 ARG cc_start: 0.7629 (mmm-85) cc_final: 0.7324 (mmm160) REVERT: B 214 ARG cc_start: 0.7213 (mmt180) cc_final: 0.6806 (mmt180) REVERT: B 304 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7363 (ttp-170) REVERT: R 254 THR cc_start: 0.6729 (m) cc_final: 0.6279 (p) REVERT: R 264 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7376 (mt) REVERT: R 328 ARG cc_start: 0.7038 (mtt180) cc_final: 0.6582 (mtt-85) REVERT: R 343 LYS cc_start: 0.7807 (tttt) cc_final: 0.7426 (tmmt) REVERT: R 364 SER cc_start: 0.8117 (m) cc_final: 0.7410 (p) REVERT: R 367 MET cc_start: 0.5283 (tmm) cc_final: 0.4908 (tmm) outliers start: 32 outliers final: 16 residues processed: 185 average time/residue: 1.6438 time to fit residues: 322.4937 Evaluate side-chains 183 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 18 ILE 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 117 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 347 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 118 optimal weight: 0.0970 chunk 97 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS B 340 ASN E 140 GLN N 3 GLN R 208 ASN R 257 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10478 Z= 0.232 Angle : 0.615 8.176 14166 Z= 0.328 Chirality : 0.048 0.629 1558 Planarity : 0.004 0.041 1775 Dihedral : 9.034 78.290 1785 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.81 % Allowed : 14.52 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.24), residues: 1251 helix: 1.72 (0.23), residues: 515 sheet: -0.11 (0.31), residues: 240 loop : -0.67 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 234 HIS 0.006 0.001 HIS A 41 PHE 0.015 0.002 PHE R 269 TYR 0.017 0.002 TYR R 56 ARG 0.003 0.001 ARG B 46 *********************** 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 198 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.239 Fit side-chains REVERT: A 296 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7164 (mp) REVERT: A 300 LYS cc_start: 0.6152 (OUTLIER) cc_final: 0.5643 (mttm) REVERT: A 370 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6506 (mm-30) REVERT: B 15 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7211 (mtpm) REVERT: B 16 ASN cc_start: 0.7394 (m-40) cc_final: 0.7180 (m110) REVERT: B 19 ARG cc_start: 0.7434 (ttp-110) cc_final: 0.7142 (ttm-80) REVERT: B 44 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.6201 (pt0) REVERT: B 197 ARG cc_start: 0.7596 (mmm-85) cc_final: 0.7281 (mmm160) REVERT: B 214 ARG cc_start: 0.7219 (mmt180) cc_final: 0.6798 (mmt180) REVERT: B 304 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7360 (ttp-170) REVERT: R 254 THR cc_start: 0.6830 (m) cc_final: 0.6372 (p) REVERT: R 264 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7419 (mt) REVERT: R 321 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6959 (ttt-90) REVERT: R 328 ARG cc_start: 0.7031 (mtt180) cc_final: 0.6576 (mtt-85) REVERT: R 343 LYS cc_start: 0.7811 (tttt) cc_final: 0.7427 (tmmt) REVERT: R 364 SER cc_start: 0.8124 (m) cc_final: 0.7426 (p) REVERT: R 367 MET cc_start: 0.5228 (tmm) cc_final: 0.4886 (tmm) outliers start: 29 outliers final: 20 residues processed: 188 average time/residue: 1.6554 time to fit residues: 330.0909 Evaluate side-chains 192 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 372 ILE 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 207 SER Chi-restraints excluded: chain B residue 304 ARG 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 211 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 349 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS B 340 ASN E 140 GLN N 3 GLN R 208 ASN R 257 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10478 Z= 0.212 Angle : 0.599 8.639 14166 Z= 0.317 Chirality : 0.046 0.570 1558 Planarity : 0.004 0.041 1775 Dihedral : 8.903 79.604 1785 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.81 % Allowed : 14.52 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1251 helix: 1.83 (0.23), residues: 516 sheet: 0.01 (0.32), residues: 243 loop : -0.71 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 PHE 0.014 0.001 PHE B 151 TYR 0.012 0.002 TYR P 37 ARG 0.003 0.000 ARG B 46 *********************** 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 198 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7184 (mp) REVERT: A 300 LYS cc_start: 0.6093 (OUTLIER) cc_final: 0.5642 (mttm) REVERT: A 370 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6486 (mm-30) REVERT: B 9 GLN cc_start: 0.6608 (OUTLIER) cc_final: 0.6226 (mt0) REVERT: B 15 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7210 (mtpm) REVERT: B 16 ASN cc_start: 0.7372 (m-40) cc_final: 0.7150 (m110) REVERT: B 19 ARG cc_start: 0.7416 (ttp-110) cc_final: 0.7117 (ttm-80) REVERT: B 44 GLN cc_start: 0.6726 (OUTLIER) cc_final: 0.6200 (pt0) REVERT: B 197 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.7280 (mmm160) REVERT: B 214 ARG cc_start: 0.7191 (mmt180) cc_final: 0.6819 (mmt180) REVERT: B 304 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7351 (ttp-170) REVERT: R 120 LYS cc_start: 0.5415 (OUTLIER) cc_final: 0.5060 (mmtm) REVERT: R 254 THR cc_start: 0.6761 (m) cc_final: 0.6330 (p) REVERT: R 264 LEU cc_start: 0.7637 (tp) cc_final: 0.7396 (mt) REVERT: R 328 ARG cc_start: 0.7006 (mtt180) cc_final: 0.6556 (mtt-85) REVERT: R 343 LYS cc_start: 0.7823 (tttt) cc_final: 0.7440 (tmmt) REVERT: R 364 SER cc_start: 0.8044 (m) cc_final: 0.7343 (p) REVERT: R 367 MET cc_start: 0.5206 (tmm) cc_final: 0.4875 (tmm) REVERT: R 368 LEU cc_start: 0.7115 (mt) cc_final: 0.6725 (tp) outliers start: 29 outliers final: 18 residues processed: 191 average time/residue: 1.6021 time to fit residues: 324.2750 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 : 1.302 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 9 GLN 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 207 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain E residue 72 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 330 THR Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 349 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 266 HIS B 340 ASN E 140 GLN N 3 GLN R 257 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10478 Z= 0.241 Angle : 0.631 8.692 14166 Z= 0.335 Chirality : 0.047 0.540 1558 Planarity : 0.004 0.041 1775 Dihedral : 9.283 83.596 1785 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.29 % Allowed : 14.42 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.24), residues: 1251 helix: 1.84 (0.23), residues: 509 sheet: -0.02 (0.31), residues: 244 loop : -0.68 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 234 HIS 0.006 0.001 HIS A 41 PHE 0.016 0.002 PHE R 269 TYR 0.014 0.002 TYR R 56 ARG 0.004 0.001 ARG A 42 *********************** 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 204 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7166 (mp) REVERT: A 300 LYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5668 (mttm) REVERT: B 9 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.6233 (mt0) REVERT: B 15 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7215 (mtpm) REVERT: B 19 ARG cc_start: 0.7438 (ttp-110) cc_final: 0.7142 (ttm-80) REVERT: B 44 GLN cc_start: 0.6724 (OUTLIER) cc_final: 0.6225 (pt0) REVERT: B 197 ARG cc_start: 0.7607 (mmm-85) cc_final: 0.7253 (mmm160) REVERT: B 214 ARG cc_start: 0.7241 (mmt180) cc_final: 0.6782 (mmt180) REVERT: B 304 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7367 (ttp-170) REVERT: G 38 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7772 (ptt) REVERT: R 120 LYS cc_start: 0.5399 (OUTLIER) cc_final: 0.5052 (mmtm) REVERT: R 254 THR cc_start: 0.6896 (m) cc_final: 0.6393 (p) REVERT: R 264 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7417 (mt) REVERT: R 321 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6949 (ttt-90) REVERT: R 328 ARG cc_start: 0.7051 (mtt180) cc_final: 0.6586 (mtt-85) REVERT: R 343 LYS cc_start: 0.7812 (tttt) cc_final: 0.7429 (tmmt) REVERT: R 364 SER cc_start: 0.8053 (m) cc_final: 0.7372 (p) REVERT: R 367 MET cc_start: 0.5235 (tmm) cc_final: 0.4892 (tmm) REVERT: R 368 LEU cc_start: 0.7029 (mt) cc_final: 0.6636 (tp) outliers start: 34 outliers final: 20 residues processed: 193 average time/residue: 1.5859 time to fit residues: 324.5628 Evaluate side-chains 194 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 1.220 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 18 ILE 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 72 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 120 LYS Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 349 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 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 B 266 HIS B 340 ASN E 140 GLN N 3 GLN R 208 ASN R 257 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.003 0.040 10478 Z= 0.185 Angle : 0.584 9.007 14166 Z= 0.307 Chirality : 0.045 0.517 1558 Planarity : 0.004 0.041 1775 Dihedral : 8.969 83.203 1785 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.52 % Allowed : 15.20 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.24), residues: 1251 helix: 1.96 (0.23), residues: 516 sheet: -0.02 (0.31), residues: 243 loop : -0.71 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.003 0.001 HIS A 41 PHE 0.014 0.001 PHE B 151 TYR 0.011 0.001 TYR R 56 ARG 0.002 0.000 ARG A 42 *********************** 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 200 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7164 (mp) REVERT: A 300 LYS cc_start: 0.6069 (OUTLIER) cc_final: 0.5654 (mttm) REVERT: A 370 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6479 (mm-30) REVERT: B 9 GLN cc_start: 0.6638 (OUTLIER) cc_final: 0.6258 (mt0) REVERT: B 15 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7262 (mtpm) REVERT: B 19 ARG cc_start: 0.7424 (ttp-110) cc_final: 0.7152 (ttm-80) REVERT: B 44 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.6185 (pt0) REVERT: B 197 ARG cc_start: 0.7591 (mmm-85) cc_final: 0.7237 (mmm160) REVERT: B 214 ARG cc_start: 0.7217 (mmt180) cc_final: 0.6828 (mmt180) REVERT: B 215 GLU cc_start: 0.7014 (mp0) cc_final: 0.6711 (mm-30) REVERT: B 304 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7351 (ttp-170) REVERT: R 48 MET cc_start: 0.4783 (ptm) cc_final: 0.4573 (ptp) REVERT: R 120 LYS cc_start: 0.5417 (OUTLIER) cc_final: 0.5078 (mmtm) REVERT: R 254 THR cc_start: 0.6789 (m) cc_final: 0.6363 (p) REVERT: R 264 LEU cc_start: 0.7611 (tp) cc_final: 0.7377 (mt) REVERT: R 328 ARG cc_start: 0.6986 (mtt180) cc_final: 0.6551 (mtt-85) REVERT: R 343 LYS cc_start: 0.7802 (tttt) cc_final: 0.7450 (tmmt) REVERT: R 364 SER cc_start: 0.8025 (m) cc_final: 0.7331 (p) REVERT: R 367 MET cc_start: 0.5242 (tmm) cc_final: 0.4893 (tmm) REVERT: R 368 LEU cc_start: 0.7012 (mt) cc_final: 0.6639 (tp) outliers start: 26 outliers final: 18 residues processed: 192 average time/residue: 1.5559 time to fit residues: 317.4885 Evaluate side-chains 192 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 18 ILE 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 72 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 208 ASN Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 347 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 16 ASN B 266 HIS B 340 ASN N 3 GLN N 13 GLN R 208 ASN R 257 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10478 Z= 0.201 Angle : 0.601 8.914 14166 Z= 0.317 Chirality : 0.046 0.516 1558 Planarity : 0.004 0.041 1775 Dihedral : 9.068 84.313 1785 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.42 % Allowed : 15.30 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.24), residues: 1251 helix: 2.02 (0.23), residues: 510 sheet: 0.06 (0.31), residues: 241 loop : -0.73 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.004 0.001 HIS A 41 PHE 0.014 0.001 PHE R 269 TYR 0.012 0.002 TYR P 37 ARG 0.003 0.000 ARG A 42 ********************** 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 195 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7174 (mp) REVERT: A 300 LYS cc_start: 0.6082 (OUTLIER) cc_final: 0.5668 (mttm) REVERT: A 370 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6478 (mm-30) REVERT: B 9 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.6252 (mt0) REVERT: B 15 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7262 (mtpm) REVERT: B 19 ARG cc_start: 0.7415 (ttp-110) cc_final: 0.7151 (ttm-80) REVERT: B 44 GLN cc_start: 0.6735 (OUTLIER) cc_final: 0.6211 (pt0) REVERT: B 197 ARG cc_start: 0.7598 (mmm-85) cc_final: 0.7244 (mmm160) REVERT: B 214 ARG cc_start: 0.7219 (mmt180) cc_final: 0.6821 (mmt180) REVERT: B 304 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7352 (ttp-170) REVERT: R 48 MET cc_start: 0.4812 (ptm) cc_final: 0.4596 (ptp) REVERT: R 120 LYS cc_start: 0.5360 (OUTLIER) cc_final: 0.5030 (mmtm) REVERT: R 254 THR cc_start: 0.6738 (m) cc_final: 0.6317 (p) REVERT: R 264 LEU cc_start: 0.7611 (tp) cc_final: 0.7383 (mt) REVERT: R 328 ARG cc_start: 0.6977 (mtt180) cc_final: 0.6559 (mtt-85) REVERT: R 343 LYS cc_start: 0.7813 (tttt) cc_final: 0.7460 (tmmt) REVERT: R 364 SER cc_start: 0.7985 (m) cc_final: 0.7300 (p) REVERT: R 367 MET cc_start: 0.5251 (tmm) cc_final: 0.4903 (tmm) REVERT: R 368 LEU cc_start: 0.7011 (mt) cc_final: 0.6618 (tp) outliers start: 25 outliers final: 16 residues processed: 187 average time/residue: 1.5730 time to fit residues: 311.9380 Evaluate side-chains 190 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 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 207 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain E residue 72 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 327 MET Chi-restraints excluded: chain R residue 347 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 0.0970 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 16 ASN B 266 HIS B 340 ASN N 3 GLN N 13 GLN R 257 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.195249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.147809 restraints weight = 17842.343| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 4.24 r_work: 0.3105 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10478 Z= 0.167 Angle : 0.576 8.842 14166 Z= 0.302 Chirality : 0.044 0.504 1558 Planarity : 0.004 0.041 1775 Dihedral : 8.805 83.852 1785 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.13 % Allowed : 15.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.24), residues: 1251 helix: 2.10 (0.23), residues: 516 sheet: 0.07 (0.32), residues: 241 loop : -0.66 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.003 0.001 HIS A 41 PHE 0.013 0.001 PHE B 151 TYR 0.012 0.001 TYR R 56 ARG 0.002 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5004.89 seconds wall clock time: 90 minutes 59.38 seconds (5459.38 seconds total)