Starting phenix.real_space_refine on Sat Dec 28 04:21:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xjh_33227/12_2024/7xjh_33227.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjh_33227/12_2024/7xjh_33227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xjh_33227/12_2024/7xjh_33227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjh_33227/12_2024/7xjh_33227.map" model { file = "/net/cci-nas-00/data/ceres_data/7xjh_33227/12_2024/7xjh_33227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjh_33227/12_2024/7xjh_33227.cif" } resolution = 3.3 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= 0.001 sd= 0.011 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4962 2.51 5 N 1378 2.21 5 O 1446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7832 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1884 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2543 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "G" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 393 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 950 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2047 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 16, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'5FW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.89, per 1000 atoms: 0.62 Number of scatterers: 7832 At special positions: 0 Unit cell: (96.3829, 120.479, 86.5255, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1446 8.00 N 1378 7.00 C 4962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 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 R 110 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS R 189 " - pdb=" SG CYS R 195 " 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=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 43.7% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.699A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 302 through 308 removed outlier: 3.662A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 307 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 341 Processing helix chain 'A' and resid 360 through 381 removed outlier: 3.888A pdb=" N ARG A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.644A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 11 through 23 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.674A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 64 removed outlier: 3.513A pdb=" N ALA R 42 " --> pdb=" O ALA R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 69 Processing helix chain 'R' and resid 70 through 90 removed outlier: 3.528A pdb=" N VAL R 74 " --> pdb=" O THR R 70 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE R 75 " --> pdb=" O MET R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 100 Processing helix chain 'R' and resid 106 through 141 removed outlier: 3.784A pdb=" N SER R 124 " --> pdb=" O CYS R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 149 Processing helix chain 'R' and resid 150 through 170 Processing helix chain 'R' and resid 170 through 175 removed outlier: 3.549A pdb=" N MET R 174 " --> pdb=" O PHE R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 192 Processing helix chain 'R' and resid 201 through 213 Processing helix chain 'R' and resid 213 through 243 Processing helix chain 'R' and resid 288 through 318 removed outlier: 3.900A pdb=" N ARG R 292 " --> pdb=" O HIS R 288 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP R 305 " --> pdb=" O PHE R 301 " (cutoff:3.500A) Proline residue: R 307 - end of helix Processing helix chain 'R' and resid 324 through 342 Processing helix chain 'R' and resid 343 through 345 No H-bonds generated for 'chain 'R' and resid 343 through 345' Processing helix chain 'R' and resid 349 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.319A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.631A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.674A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.725A 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: 6.043A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150 removed outlier: 4.053A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.057A 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: 6.684A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.036A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.423A 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: 4.259A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (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 11 through 12 removed outlier: 6.244A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1200 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: 2.28 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2581 1.34 - 1.46: 1625 1.46 - 1.58: 3719 1.58 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 7986 Sorted by residual: bond pdb=" CA SER N 21 " pdb=" CB SER N 21 " ideal model delta sigma weight residual 1.532 1.486 0.046 1.74e-02 3.30e+03 6.99e+00 bond pdb=" CAO 5FW R 401 " pdb=" OAC 5FW R 401 " ideal model delta sigma weight residual 1.351 1.400 -0.049 2.00e-02 2.50e+03 6.06e+00 bond pdb=" CAM 5FW R 401 " pdb=" OAB 5FW R 401 " ideal model delta sigma weight residual 1.353 1.401 -0.048 2.00e-02 2.50e+03 5.66e+00 bond pdb=" C LEU R 306 " pdb=" N PRO R 307 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.30e-02 5.92e+03 2.00e+00 bond pdb=" N SER N 21 " pdb=" CA SER N 21 " ideal model delta sigma weight residual 1.454 1.470 -0.016 1.19e-02 7.06e+03 1.79e+00 ... (remaining 7981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 10580 1.53 - 3.07: 224 3.07 - 4.60: 38 4.60 - 6.13: 13 6.13 - 7.67: 3 Bond angle restraints: 10858 Sorted by residual: angle pdb=" N PHE A 222 " pdb=" CA PHE A 222 " pdb=" C PHE A 222 " ideal model delta sigma weight residual 108.55 113.15 -4.60 1.62e+00 3.81e-01 8.07e+00 angle pdb=" N GLU A 16 " pdb=" CA GLU A 16 " pdb=" CB GLU A 16 " ideal model delta sigma weight residual 110.28 114.64 -4.36 1.55e+00 4.16e-01 7.90e+00 angle pdb=" CA SER N 21 " pdb=" C SER N 21 " pdb=" O SER N 21 " ideal model delta sigma weight residual 121.16 118.03 3.13 1.13e+00 7.83e-01 7.66e+00 angle pdb=" C LEU N 20 " pdb=" N SER N 21 " pdb=" CA SER N 21 " ideal model delta sigma weight residual 122.87 118.94 3.93 1.61e+00 3.86e-01 5.95e+00 angle pdb=" C LEU R 89 " pdb=" N VAL R 90 " pdb=" CA VAL R 90 " ideal model delta sigma weight residual 122.63 119.81 2.82 1.19e+00 7.06e-01 5.60e+00 ... (remaining 10853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4301 17.97 - 35.93: 382 35.93 - 53.90: 58 53.90 - 71.87: 9 71.87 - 89.83: 8 Dihedral angle restraints: 4758 sinusoidal: 1782 harmonic: 2976 Sorted by residual: dihedral pdb=" CB CYS R 189 " pdb=" SG CYS R 189 " pdb=" SG CYS R 195 " pdb=" CB CYS R 195 " ideal model delta sinusoidal sigma weight residual -86.00 -133.54 47.54 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 134.21 -41.21 1 1.00e+01 1.00e-02 2.38e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual -180.00 -157.03 -22.97 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 4755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 967 0.045 - 0.090: 220 0.090 - 0.134: 67 0.134 - 0.179: 2 0.179 - 0.224: 2 Chirality restraints: 1258 Sorted by residual: chirality pdb=" CAE 5FW R 401 " pdb=" CAF 5FW R 401 " pdb=" CAH 5FW R 401 " pdb=" OAA 5FW R 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.52 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB THR A 315 " pdb=" CA THR A 315 " pdb=" OG1 THR A 315 " pdb=" CG2 THR A 315 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 1255 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 215 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO R 216 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO R 216 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 216 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 323 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO R 324 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO R 324 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 324 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 192 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO R 193 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO R 193 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 193 " 0.022 5.00e-02 4.00e+02 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1016 2.75 - 3.29: 7524 3.29 - 3.83: 13177 3.83 - 4.36: 15228 4.36 - 4.90: 27153 Nonbonded interactions: 64098 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.218 3.040 nonbonded pdb=" OD2 ASP A 33 " pdb=" NZ LYS B 78 " model vdw 2.223 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.226 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.228 3.040 nonbonded pdb=" O GLU B 226 " pdb=" NH2 ARG N 98 " model vdw 2.252 3.120 ... (remaining 64093 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=1.00 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: 0.170 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.650 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 : 0.003 0.049 7986 Z= 0.194 Angle : 0.584 7.667 10858 Z= 0.315 Chirality : 0.042 0.224 1258 Planarity : 0.004 0.045 1390 Dihedral : 14.021 89.834 2820 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 0.45 (0.27), residues: 1011 helix: 2.43 (0.26), residues: 377 sheet: -0.72 (0.33), residues: 212 loop : -1.14 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.023 0.002 PHE A 222 TYR 0.011 0.001 TYR B 59 ARG 0.007 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7055 (mtmt) cc_final: 0.6774 (mtmt) REVERT: A 32 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7353 (mtpt) REVERT: A 34 LYS cc_start: 0.8052 (ttpp) cc_final: 0.7769 (tttt) REVERT: A 213 GLN cc_start: 0.7742 (tt0) cc_final: 0.7514 (tt0) REVERT: A 252 ASP cc_start: 0.7055 (t70) cc_final: 0.6826 (t70) REVERT: A 304 GLU cc_start: 0.7674 (pm20) cc_final: 0.7462 (pm20) REVERT: B 42 ARG cc_start: 0.7577 (tmt170) cc_final: 0.6922 (tpt170) REVERT: B 175 GLN cc_start: 0.7772 (mt0) cc_final: 0.7544 (mt0) REVERT: B 226 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8450 (mt-10) REVERT: N 20 LEU cc_start: 0.8027 (mt) cc_final: 0.7764 (mt) REVERT: N 21 SER cc_start: 0.8305 (m) cc_final: 0.7963 (p) REVERT: N 77 ASN cc_start: 0.6830 (m-40) cc_final: 0.6525 (m-40) REVERT: R 236 ARG cc_start: 0.6685 (mtm110) cc_final: 0.6406 (mtm110) REVERT: R 240 ARG cc_start: 0.7363 (tmm-80) cc_final: 0.7003 (ttm170) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2513 time to fit residues: 53.2637 Evaluate side-chains 129 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN B 220 GLN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7986 Z= 0.194 Angle : 0.542 7.762 10858 Z= 0.283 Chirality : 0.041 0.152 1258 Planarity : 0.004 0.047 1390 Dihedral : 4.263 28.484 1122 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.74 % Allowed : 6.50 % Favored : 92.76 % 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: 0.60 (0.27), residues: 1011 helix: 2.44 (0.26), residues: 379 sheet: -0.49 (0.34), residues: 213 loop : -1.05 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.006 0.001 HIS A 347 PHE 0.014 0.001 PHE A 212 TYR 0.013 0.001 TYR A 37 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.949 Fit side-chains REVERT: A 32 LYS cc_start: 0.7937 (mtpt) cc_final: 0.7441 (mtpt) REVERT: A 34 LYS cc_start: 0.8024 (ttpp) cc_final: 0.7790 (tttt) REVERT: A 35 GLN cc_start: 0.7313 (pt0) cc_final: 0.7071 (pt0) REVERT: A 252 ASP cc_start: 0.7095 (t70) cc_final: 0.6868 (t70) REVERT: A 304 GLU cc_start: 0.7826 (pm20) cc_final: 0.7591 (pm20) REVERT: A 308 TYR cc_start: 0.7632 (t80) cc_final: 0.6945 (t80) REVERT: B 42 ARG cc_start: 0.7579 (tmt170) cc_final: 0.6928 (tpt170) REVERT: B 175 GLN cc_start: 0.7626 (mt0) cc_final: 0.7397 (mt0) REVERT: B 226 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8211 (mt-10) REVERT: N 20 LEU cc_start: 0.7991 (mt) cc_final: 0.7739 (mt) REVERT: N 77 ASN cc_start: 0.6773 (m-40) cc_final: 0.6515 (m-40) REVERT: R 236 ARG cc_start: 0.6592 (mtm110) cc_final: 0.6347 (mtm110) outliers start: 6 outliers final: 3 residues processed: 138 average time/residue: 0.2426 time to fit residues: 43.6729 Evaluate side-chains 129 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 268 ASN B 220 GLN B 230 ASN G 59 ASN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7986 Z= 0.201 Angle : 0.536 8.205 10858 Z= 0.278 Chirality : 0.041 0.150 1258 Planarity : 0.004 0.047 1390 Dihedral : 4.269 29.181 1122 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.35 % Allowed : 10.43 % Favored : 88.22 % 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 (0.27), residues: 1011 helix: 2.39 (0.26), residues: 384 sheet: -0.56 (0.34), residues: 206 loop : -0.97 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.005 0.001 HIS A 347 PHE 0.019 0.002 PHE N 108 TYR 0.012 0.001 TYR A 37 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.845 Fit side-chains REVERT: A 32 LYS cc_start: 0.7983 (mtpt) cc_final: 0.7459 (mtpt) REVERT: A 34 LYS cc_start: 0.8069 (ttpp) cc_final: 0.7843 (tttt) REVERT: A 230 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7398 (mt-10) REVERT: A 252 ASP cc_start: 0.7070 (t70) cc_final: 0.6802 (t70) REVERT: A 304 GLU cc_start: 0.7815 (pm20) cc_final: 0.7594 (pm20) REVERT: A 329 TYR cc_start: 0.8428 (m-80) cc_final: 0.8019 (m-80) REVERT: B 42 ARG cc_start: 0.7605 (tmt170) cc_final: 0.6922 (tpt170) REVERT: B 175 GLN cc_start: 0.7594 (mt0) cc_final: 0.7359 (mt0) REVERT: B 226 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8241 (mt-10) REVERT: B 256 ARG cc_start: 0.7907 (mtm110) cc_final: 0.7189 (mtm110) REVERT: B 259 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7666 (mm-40) REVERT: N 20 LEU cc_start: 0.7964 (mt) cc_final: 0.7712 (mt) REVERT: N 65 LYS cc_start: 0.6473 (ttmm) cc_final: 0.6220 (tptp) REVERT: R 68 LEU cc_start: 0.7641 (mt) cc_final: 0.7419 (mt) outliers start: 11 outliers final: 9 residues processed: 132 average time/residue: 0.2931 time to fit residues: 50.5049 Evaluate side-chains 127 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 288 HIS Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 26 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7986 Z= 0.150 Angle : 0.506 8.567 10858 Z= 0.263 Chirality : 0.041 0.298 1258 Planarity : 0.004 0.044 1390 Dihedral : 4.085 28.000 1122 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.35 % Allowed : 12.39 % Favored : 86.26 % 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: 0.75 (0.27), residues: 1011 helix: 2.62 (0.26), residues: 379 sheet: -0.46 (0.33), residues: 216 loop : -1.00 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 347 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR A 37 ARG 0.003 0.000 ARG R 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.847 Fit side-chains REVERT: A 32 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7497 (mtpt) REVERT: A 252 ASP cc_start: 0.7039 (t70) cc_final: 0.6763 (t70) REVERT: A 304 GLU cc_start: 0.7804 (pm20) cc_final: 0.7570 (pm20) REVERT: A 329 TYR cc_start: 0.8367 (m-80) cc_final: 0.7985 (m-80) REVERT: B 42 ARG cc_start: 0.7571 (tmt170) cc_final: 0.6855 (tpt170) REVERT: B 175 GLN cc_start: 0.7625 (mt0) cc_final: 0.7415 (mt0) REVERT: B 256 ARG cc_start: 0.7886 (mtm110) cc_final: 0.7072 (mtm110) REVERT: B 259 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7688 (mm-40) REVERT: B 329 THR cc_start: 0.9077 (m) cc_final: 0.8586 (p) REVERT: N 20 LEU cc_start: 0.7996 (mt) cc_final: 0.7734 (mt) REVERT: N 65 LYS cc_start: 0.6481 (ttmm) cc_final: 0.6211 (tptp) REVERT: R 135 ARG cc_start: 0.8203 (ptp90) cc_final: 0.7932 (mtt180) outliers start: 11 outliers final: 6 residues processed: 138 average time/residue: 0.2358 time to fit residues: 42.5697 Evaluate side-chains 127 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 126 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN N 77 ASN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7986 Z= 0.216 Angle : 0.541 8.335 10858 Z= 0.280 Chirality : 0.042 0.316 1258 Planarity : 0.004 0.046 1390 Dihedral : 4.229 29.302 1122 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.96 % Allowed : 12.88 % Favored : 85.15 % 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: 0.66 (0.27), residues: 1011 helix: 2.33 (0.26), residues: 390 sheet: -0.34 (0.33), residues: 213 loop : -1.02 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.005 0.001 HIS A 347 PHE 0.015 0.002 PHE R 308 TYR 0.013 0.001 TYR A 37 ARG 0.004 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.834 Fit side-chains REVERT: A 32 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7436 (mtpt) REVERT: A 252 ASP cc_start: 0.7069 (t70) cc_final: 0.6783 (t70) REVERT: A 304 GLU cc_start: 0.7788 (pm20) cc_final: 0.7550 (pm20) REVERT: A 329 TYR cc_start: 0.8418 (m-80) cc_final: 0.8021 (m-80) REVERT: B 42 ARG cc_start: 0.7588 (tmt170) cc_final: 0.6850 (tpt170) REVERT: B 175 GLN cc_start: 0.7633 (mt0) cc_final: 0.7412 (mt0) REVERT: B 256 ARG cc_start: 0.7931 (mtm110) cc_final: 0.7252 (mtm110) REVERT: B 259 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7758 (mm-40) REVERT: N 20 LEU cc_start: 0.7980 (mt) cc_final: 0.7681 (mt) REVERT: N 46 GLU cc_start: 0.8021 (pt0) cc_final: 0.7687 (pt0) REVERT: N 65 LYS cc_start: 0.6518 (ttmm) cc_final: 0.6249 (tptp) REVERT: N 108 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7341 (t80) outliers start: 16 outliers final: 12 residues processed: 131 average time/residue: 0.2479 time to fit residues: 42.2974 Evaluate side-chains 128 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 288 HIS Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN N 77 ASN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7986 Z= 0.252 Angle : 0.562 8.359 10858 Z= 0.293 Chirality : 0.042 0.273 1258 Planarity : 0.004 0.048 1390 Dihedral : 4.386 29.981 1122 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.31 % Allowed : 13.50 % Favored : 83.19 % 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: 0.54 (0.26), residues: 1011 helix: 2.23 (0.26), residues: 388 sheet: -0.36 (0.34), residues: 205 loop : -1.09 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.006 0.001 HIS A 347 PHE 0.017 0.002 PHE R 308 TYR 0.013 0.002 TYR A 329 ARG 0.005 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.907 Fit side-chains REVERT: A 32 LYS cc_start: 0.7944 (mtpt) cc_final: 0.7448 (mtpt) REVERT: A 252 ASP cc_start: 0.7128 (t70) cc_final: 0.6785 (t70) REVERT: B 42 ARG cc_start: 0.7589 (tmt170) cc_final: 0.6876 (tpt170) REVERT: B 175 GLN cc_start: 0.7651 (mt0) cc_final: 0.7429 (mt0) REVERT: B 226 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8182 (mt-10) REVERT: B 256 ARG cc_start: 0.7946 (mtm110) cc_final: 0.7242 (mtm110) REVERT: B 259 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7773 (mm-40) REVERT: N 20 LEU cc_start: 0.7954 (mt) cc_final: 0.7686 (mt) REVERT: N 46 GLU cc_start: 0.8125 (pt0) cc_final: 0.7814 (pt0) REVERT: N 65 LYS cc_start: 0.6559 (ttmm) cc_final: 0.6290 (tptp) outliers start: 27 outliers final: 20 residues processed: 135 average time/residue: 0.2287 time to fit residues: 41.1799 Evaluate side-chains 135 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 288 HIS Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 344 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN N 77 ASN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7986 Z= 0.228 Angle : 0.553 8.581 10858 Z= 0.289 Chirality : 0.043 0.425 1258 Planarity : 0.004 0.048 1390 Dihedral : 4.350 30.201 1122 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.70 % Allowed : 14.48 % Favored : 82.82 % 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: 0.56 (0.26), residues: 1011 helix: 2.27 (0.26), residues: 388 sheet: -0.43 (0.34), residues: 205 loop : -1.05 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.006 0.001 HIS A 347 PHE 0.016 0.002 PHE R 308 TYR 0.013 0.001 TYR A 37 ARG 0.004 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.901 Fit side-chains REVERT: A 32 LYS cc_start: 0.7938 (mtpt) cc_final: 0.7442 (mtpt) REVERT: A 252 ASP cc_start: 0.7159 (t70) cc_final: 0.6810 (t70) REVERT: B 42 ARG cc_start: 0.7653 (tmt170) cc_final: 0.6895 (tpt170) REVERT: B 175 GLN cc_start: 0.7644 (mt0) cc_final: 0.7426 (mt0) REVERT: B 226 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8180 (mt-10) REVERT: B 256 ARG cc_start: 0.7947 (mtm110) cc_final: 0.7262 (mtm110) REVERT: B 259 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7764 (mm-40) REVERT: N 20 LEU cc_start: 0.7945 (mt) cc_final: 0.7671 (mt) REVERT: N 46 GLU cc_start: 0.8119 (pt0) cc_final: 0.7810 (pt0) REVERT: N 65 LYS cc_start: 0.6568 (ttmm) cc_final: 0.6297 (tptp) REVERT: N 108 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7511 (t80) outliers start: 22 outliers final: 18 residues processed: 134 average time/residue: 0.2255 time to fit residues: 40.1551 Evaluate side-chains 138 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 288 HIS Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 88 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN N 77 ASN N 123 GLN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7986 Z= 0.156 Angle : 0.521 8.894 10858 Z= 0.270 Chirality : 0.041 0.373 1258 Planarity : 0.004 0.046 1390 Dihedral : 4.105 27.974 1122 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.21 % Allowed : 14.97 % Favored : 82.82 % 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: 0.75 (0.27), residues: 1011 helix: 2.54 (0.26), residues: 385 sheet: -0.40 (0.33), residues: 212 loop : -1.01 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.015 0.001 PHE A 212 TYR 0.013 0.001 TYR A 37 ARG 0.002 0.000 ARG R 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.880 Fit side-chains REVERT: A 32 LYS cc_start: 0.7907 (mtpt) cc_final: 0.7428 (mtpt) REVERT: A 252 ASP cc_start: 0.7025 (t70) cc_final: 0.6681 (t70) REVERT: A 308 TYR cc_start: 0.7576 (t80) cc_final: 0.7164 (t80) REVERT: A 329 TYR cc_start: 0.8348 (m-80) cc_final: 0.7928 (m-80) REVERT: B 42 ARG cc_start: 0.7630 (tmt170) cc_final: 0.6879 (tpt170) REVERT: B 256 ARG cc_start: 0.7860 (mtm110) cc_final: 0.7194 (mtm110) REVERT: B 259 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7778 (mm-40) REVERT: B 298 ASP cc_start: 0.7675 (t0) cc_final: 0.7420 (t70) REVERT: B 329 THR cc_start: 0.9032 (m) cc_final: 0.8606 (p) REVERT: N 20 LEU cc_start: 0.7955 (mt) cc_final: 0.7664 (mt) REVERT: N 46 GLU cc_start: 0.8141 (pt0) cc_final: 0.7823 (pt0) REVERT: N 60 TYR cc_start: 0.8517 (m-80) cc_final: 0.8267 (m-80) REVERT: N 65 LYS cc_start: 0.6561 (ttmm) cc_final: 0.6275 (tptp) outliers start: 18 outliers final: 14 residues processed: 138 average time/residue: 0.2555 time to fit residues: 46.3045 Evaluate side-chains 140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN N 82 GLN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7986 Z= 0.258 Angle : 0.579 8.461 10858 Z= 0.301 Chirality : 0.044 0.435 1258 Planarity : 0.004 0.048 1390 Dihedral : 4.396 29.874 1122 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.58 % Allowed : 14.11 % Favored : 83.31 % 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 (0.27), residues: 1011 helix: 2.30 (0.26), residues: 388 sheet: -0.48 (0.34), residues: 207 loop : -0.98 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.006 0.001 HIS A 347 PHE 0.018 0.002 PHE R 308 TYR 0.013 0.002 TYR A 329 ARG 0.005 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.884 Fit side-chains REVERT: A 32 LYS cc_start: 0.7922 (mtpt) cc_final: 0.7445 (mtpt) REVERT: A 252 ASP cc_start: 0.7042 (t70) cc_final: 0.6696 (t70) REVERT: B 42 ARG cc_start: 0.7614 (tmt170) cc_final: 0.6911 (tpt170) REVERT: B 256 ARG cc_start: 0.7890 (mtm110) cc_final: 0.7200 (mtm110) REVERT: B 259 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7793 (mm-40) REVERT: B 298 ASP cc_start: 0.7788 (t0) cc_final: 0.7509 (t70) REVERT: N 20 LEU cc_start: 0.7940 (mt) cc_final: 0.7663 (mt) REVERT: N 46 GLU cc_start: 0.8094 (pt0) cc_final: 0.7805 (pt0) REVERT: N 108 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7514 (t80) outliers start: 21 outliers final: 18 residues processed: 135 average time/residue: 0.2464 time to fit residues: 43.7620 Evaluate side-chains 140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7986 Z= 0.289 Angle : 0.601 10.322 10858 Z= 0.313 Chirality : 0.045 0.453 1258 Planarity : 0.004 0.049 1390 Dihedral : 4.524 30.601 1122 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.33 % Allowed : 14.23 % Favored : 83.44 % 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: 0.39 (0.26), residues: 1011 helix: 2.04 (0.26), residues: 388 sheet: -0.52 (0.34), residues: 204 loop : -1.04 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 99 HIS 0.006 0.001 HIS A 347 PHE 0.018 0.002 PHE R 308 TYR 0.014 0.002 TYR A 329 ARG 0.006 0.000 ARG N 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.944 Fit side-chains REVERT: A 32 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7449 (mtpt) REVERT: A 252 ASP cc_start: 0.7066 (t70) cc_final: 0.6713 (t70) REVERT: B 42 ARG cc_start: 0.7631 (tmt170) cc_final: 0.6952 (tpt170) REVERT: B 256 ARG cc_start: 0.7929 (mtm110) cc_final: 0.7181 (mtm110) REVERT: B 259 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7789 (mm-40) REVERT: B 298 ASP cc_start: 0.7826 (t0) cc_final: 0.7548 (t70) REVERT: G 38 MET cc_start: 0.6968 (mtt) cc_final: 0.6768 (mtp) REVERT: N 20 LEU cc_start: 0.7940 (mt) cc_final: 0.7673 (mt) REVERT: N 46 GLU cc_start: 0.8093 (pt0) cc_final: 0.7794 (pt0) REVERT: N 60 TYR cc_start: 0.8613 (m-80) cc_final: 0.8272 (m-80) REVERT: N 65 LYS cc_start: 0.6624 (ttmm) cc_final: 0.6313 (tptp) outliers start: 19 outliers final: 18 residues processed: 132 average time/residue: 0.2413 time to fit residues: 41.8696 Evaluate side-chains 140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 4 optimal weight: 0.2980 chunk 57 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN N 82 GLN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.154285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.120067 restraints weight = 8870.782| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.82 r_work: 0.3150 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7986 Z= 0.147 Angle : 0.528 9.193 10858 Z= 0.275 Chirality : 0.042 0.430 1258 Planarity : 0.004 0.046 1390 Dihedral : 4.154 27.792 1122 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.60 % Allowed : 14.72 % Favored : 83.68 % 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: 0.64 (0.27), residues: 1011 helix: 2.40 (0.26), residues: 385 sheet: -0.46 (0.34), residues: 213 loop : -0.99 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.015 0.001 PHE A 212 TYR 0.013 0.001 TYR A 37 ARG 0.004 0.000 ARG R 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1964.56 seconds wall clock time: 36 minutes 45.22 seconds (2205.22 seconds total)