Starting phenix.real_space_refine on Sat Dec 28 17:19:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e3y_27873/12_2024/8e3y_27873.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e3y_27873/12_2024/8e3y_27873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e3y_27873/12_2024/8e3y_27873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e3y_27873/12_2024/8e3y_27873.map" model { file = "/net/cci-nas-00/data/ceres_data/8e3y_27873/12_2024/8e3y_27873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e3y_27873/12_2024/8e3y_27873.cif" } resolution = 2.3 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= 0.000 sd= 0.002 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 60 5.16 5 C 5685 2.51 5 N 1559 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 8966 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1856 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1844 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 221, 1844 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 3 bond proxies already assigned to first conformer: 1864 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} 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: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2890 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 357} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 358 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 358 " occ=0.50 Time building chain proxies: 6.54, per 1000 atoms: 0.73 Number of scatterers: 8966 At special positions: 0 Unit cell: (89.7, 99.45, 163.8, 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 60 16.00 O 1662 8.00 N 1559 7.00 C 5685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 50 " - pdb=" SG CYS R 72 " distance=1.98 Simple disulfide: pdb=" SG CYS R 63 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 86 " - pdb=" SG CYS R 122 " distance=2.03 Simple disulfide: pdb=" SG CYS R 215 " - pdb=" SG CYS R 285 " 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: 2.27 Conformation dependent library (CDL) restraints added in 1.3 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 11 sheets defined 43.8% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.667A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.081A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.713A 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 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.623A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 27 Processing helix chain 'R' and resid 37 through 54 removed outlier: 3.514A pdb=" N GLN R 41 " --> pdb=" O CYS R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 94 removed outlier: 4.149A pdb=" N PHE R 93 " --> pdb=" O ILE R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 121 removed outlier: 3.674A pdb=" N ILE R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 127 removed outlier: 3.539A pdb=" N ASP R 126 " --> pdb=" O CYS R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 167 removed outlier: 3.709A pdb=" N VAL R 159 " --> pdb=" O ALA R 155 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE R 167 " --> pdb=" O ILE R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 171 Processing helix chain 'R' and resid 172 through 200 Processing helix chain 'R' and resid 205 through 210 removed outlier: 3.914A pdb=" N SER R 209 " --> pdb=" O SER R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 246 Processing helix chain 'R' and resid 250 through 253 Processing helix chain 'R' and resid 254 through 281 removed outlier: 4.431A pdb=" N VAL R 265 " --> pdb=" O ILE R 261 " (cutoff:3.500A) Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 293 through 324 removed outlier: 4.002A pdb=" N ILE R 297 " --> pdb=" O LEU R 293 " (cutoff:3.500A) Proline residue: R 300 - end of helix removed outlier: 3.595A pdb=" N ARG R 324 " --> pdb=" O LEU R 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 351 Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 352 through 356 Processing helix chain 'R' and resid 365 through 375 removed outlier: 3.665A pdb=" N LYS R 369 " --> pdb=" O LYS R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 376 through 378 No H-bonds generated for 'chain 'R' and resid 376 through 378' Processing helix chain 'R' and resid 379 through 388 Processing helix chain 'R' and resid 392 through 407 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.424A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.260A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.833A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.031A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.433A 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: 6.671A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.984A 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: 3.512A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.676A 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: 6.659A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.700A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 303 " --> 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 11 removed outlier: 5.631A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 82 through 85 461 hydrogen bonds defined for protein. 1299 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: 2.65 Time building geometry restraints manager: 2.65 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: 2912 1.34 - 1.46: 1510 1.46 - 1.57: 4639 1.57 - 1.69: 0 1.69 - 1.81: 83 Bond restraints: 9144 Sorted by residual: bond pdb=" N VAL P 19 " pdb=" CA VAL P 19 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.77e+00 bond pdb=" N ILE R 177 " pdb=" CA ILE R 177 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.26e-02 6.30e+03 8.10e+00 bond pdb=" N VAL R 235 " pdb=" CA VAL R 235 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.71e+00 bond pdb=" N PHE R 93 " pdb=" CA PHE R 93 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.32e-02 5.74e+03 7.57e+00 bond pdb=" N LEU R 349 " pdb=" CA LEU R 349 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.33e-02 5.65e+03 7.54e+00 ... (remaining 9139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 11643 1.13 - 2.26: 530 2.26 - 3.39: 168 3.39 - 4.51: 21 4.51 - 5.64: 14 Bond angle restraints: 12376 Sorted by residual: angle pdb=" N ALA R 129 " pdb=" CA ALA R 129 " pdb=" C ALA R 129 " ideal model delta sigma weight residual 111.71 106.46 5.25 1.15e+00 7.56e-01 2.09e+01 angle pdb=" N LEU R 233 " pdb=" CA LEU R 233 " pdb=" C LEU R 233 " ideal model delta sigma weight residual 111.36 106.41 4.95 1.09e+00 8.42e-01 2.06e+01 angle pdb=" N PHE R 350 " pdb=" CA PHE R 350 " pdb=" C PHE R 350 " ideal model delta sigma weight residual 114.31 108.69 5.62 1.29e+00 6.01e-01 1.90e+01 angle pdb=" N PHE R 182 " pdb=" CA PHE R 182 " pdb=" C PHE R 182 " ideal model delta sigma weight residual 112.23 107.79 4.44 1.26e+00 6.30e-01 1.24e+01 angle pdb=" N LEU R 181 " pdb=" CA LEU R 181 " pdb=" C LEU R 181 " ideal model delta sigma weight residual 111.28 107.73 3.55 1.09e+00 8.42e-01 1.06e+01 ... (remaining 12371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 4934 16.94 - 33.89: 410 33.89 - 50.83: 64 50.83 - 67.78: 12 67.78 - 84.72: 7 Dihedral angle restraints: 5427 sinusoidal: 2117 harmonic: 3310 Sorted by residual: dihedral pdb=" CB CYS R 50 " pdb=" SG CYS R 50 " pdb=" SG CYS R 72 " pdb=" CB CYS R 72 " ideal model delta sinusoidal sigma weight residual -86.00 -145.03 59.03 1 1.00e+01 1.00e-02 4.66e+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 -86.00 -127.78 41.78 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CB CYS R 86 " pdb=" SG CYS R 86 " pdb=" SG CYS R 122 " pdb=" CB CYS R 122 " ideal model delta sinusoidal sigma weight residual 93.00 133.96 -40.96 1 1.00e+01 1.00e-02 2.35e+01 ... (remaining 5424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1013 0.045 - 0.091: 262 0.091 - 0.136: 74 0.136 - 0.182: 13 0.182 - 0.227: 7 Chirality restraints: 1369 Sorted by residual: chirality pdb=" CA ASN R 175 " pdb=" N ASN R 175 " pdb=" C ASN R 175 " pdb=" CB ASN R 175 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ILE R 177 " pdb=" N ILE R 177 " pdb=" C ILE R 177 " pdb=" CB ILE R 177 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LEU R 233 " pdb=" N LEU R 233 " pdb=" C LEU R 233 " pdb=" CB LEU R 233 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1366 not shown) Planarity restraints: 1583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO G 53 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " -0.033 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 332 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 334 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO R 335 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO R 335 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 335 " 0.023 5.00e-02 4.00e+02 ... (remaining 1580 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1594 2.77 - 3.30: 8672 3.30 - 3.83: 15280 3.83 - 4.37: 18618 4.37 - 4.90: 31213 Nonbonded interactions: 75377 Sorted by model distance: nonbonded pdb=" O PRO R 300 " pdb=" OG1 THR R 303 " model vdw 2.237 3.040 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.259 3.120 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.271 3.040 nonbonded pdb=" OE2 GLU A 230 " pdb=" OG SER N 112 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.303 3.040 ... (remaining 75372 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: 1.970 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: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 24.620 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 0.037 9144 Z= 0.206 Angle : 0.599 5.643 12376 Z= 0.404 Chirality : 0.047 0.227 1369 Planarity : 0.004 0.058 1583 Dihedral : 12.649 84.724 3276 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.11 % Allowed : 0.53 % Favored : 99.36 % 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: 1.26 (0.25), residues: 1124 helix: 2.05 (0.25), residues: 445 sheet: 0.50 (0.33), residues: 224 loop : -0.15 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.013 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.011 0.001 TYR R 388 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 1.039 Fit side-chains REVERT: B 6 GLN cc_start: 0.7495 (pp30) cc_final: 0.7293 (pp30) REVERT: G 20 LYS cc_start: 0.8426 (mtmt) cc_final: 0.7861 (mtmt) REVERT: R 252 ARG cc_start: 0.6712 (tpt90) cc_final: 0.6467 (tpt170) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 1.5567 time to fit residues: 273.1430 Evaluate side-chains 139 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 176 GLN B 237 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN R 321 GLN R 353 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9144 Z= 0.266 Angle : 0.564 8.437 12376 Z= 0.307 Chirality : 0.044 0.141 1369 Planarity : 0.004 0.051 1583 Dihedral : 4.313 22.346 1244 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.17 % Allowed : 9.32 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.67 (0.25), residues: 1124 helix: 2.59 (0.24), residues: 445 sheet: 0.66 (0.33), residues: 223 loop : -0.12 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.024 0.001 HIS A 357 PHE 0.014 0.002 PHE R 382 TYR 0.030 0.002 TYR R 146 ARG 0.006 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 1.037 Fit side-chains REVERT: A 17 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7567 (ptmm) REVERT: A 314 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: B 134 ARG cc_start: 0.7492 (ptp90) cc_final: 0.7246 (ptp90) REVERT: G 17 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7885 (mm-30) REVERT: G 20 LYS cc_start: 0.8587 (mtmt) cc_final: 0.8258 (mtmt) REVERT: N 43 LYS cc_start: 0.8449 (mttm) cc_final: 0.8207 (mttp) REVERT: R 252 ARG cc_start: 0.6857 (tpt90) cc_final: 0.6570 (tpt170) outliers start: 11 outliers final: 3 residues processed: 151 average time/residue: 1.5432 time to fit residues: 246.1536 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 139 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9144 Z= 0.221 Angle : 0.525 7.280 12376 Z= 0.287 Chirality : 0.042 0.137 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.318 21.993 1244 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.48 % Allowed : 9.96 % Favored : 88.56 % 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: 1.68 (0.25), residues: 1124 helix: 2.61 (0.24), residues: 445 sheet: 0.73 (0.33), residues: 231 loop : -0.20 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 256 HIS 0.018 0.001 HIS A 357 PHE 0.014 0.001 PHE R 382 TYR 0.025 0.001 TYR R 146 ARG 0.005 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.985 Fit side-chains REVERT: A 17 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7579 (ptmm) REVERT: A 20 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6946 (mtm-85) REVERT: A 59 GLN cc_start: 0.8230 (tp40) cc_final: 0.7678 (mm-40) REVERT: A 314 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: G 20 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8264 (mtmt) REVERT: N 3 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: N 43 LYS cc_start: 0.8507 (mttm) cc_final: 0.8261 (mttp) REVERT: R 252 ARG cc_start: 0.6806 (tpt90) cc_final: 0.6500 (tpt170) outliers start: 14 outliers final: 3 residues processed: 146 average time/residue: 1.5773 time to fit residues: 243.0047 Evaluate side-chains 149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 0.0270 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 237 ASN N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9144 Z= 0.220 Angle : 0.523 6.921 12376 Z= 0.286 Chirality : 0.042 0.136 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.322 21.380 1244 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.59 % Allowed : 11.23 % Favored : 87.18 % 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: 1.70 (0.25), residues: 1124 helix: 2.65 (0.24), residues: 445 sheet: 0.75 (0.33), residues: 231 loop : -0.21 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 256 HIS 0.016 0.001 HIS A 357 PHE 0.014 0.001 PHE R 222 TYR 0.024 0.001 TYR R 146 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 1.044 Fit side-chains REVERT: A 17 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7553 (ptmm) REVERT: A 59 GLN cc_start: 0.8222 (tp40) cc_final: 0.7679 (mm-40) REVERT: B 266 HIS cc_start: 0.8155 (t-170) cc_final: 0.7933 (t-170) REVERT: G 17 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7832 (mm-30) REVERT: G 20 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8182 (mtmt) REVERT: N 3 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8067 (tt0) REVERT: R 252 ARG cc_start: 0.6805 (tpt90) cc_final: 0.6484 (tpt170) REVERT: R 338 ARG cc_start: 0.7071 (tpt170) cc_final: 0.6718 (tpt170) outliers start: 15 outliers final: 2 residues processed: 144 average time/residue: 1.6157 time to fit residues: 245.0784 Evaluate side-chains 141 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 237 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN R 363 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9144 Z= 0.350 Angle : 0.585 7.222 12376 Z= 0.320 Chirality : 0.045 0.147 1369 Planarity : 0.005 0.053 1583 Dihedral : 4.626 22.171 1244 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.38 % Allowed : 12.08 % Favored : 86.55 % 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: 1.64 (0.25), residues: 1124 helix: 2.53 (0.24), residues: 445 sheet: 0.84 (0.33), residues: 229 loop : -0.24 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 256 HIS 0.019 0.002 HIS A 357 PHE 0.018 0.002 PHE R 222 TYR 0.024 0.002 TYR R 146 ARG 0.006 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.057 Fit side-chains REVERT: A 17 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7597 (ptmm) REVERT: A 59 GLN cc_start: 0.8241 (tp40) cc_final: 0.7698 (mm-40) REVERT: B 59 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.8844 (m-80) REVERT: G 17 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7773 (mm-30) REVERT: G 20 LYS cc_start: 0.8588 (mtmt) cc_final: 0.8160 (mtmt) REVERT: N 3 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: N 89 GLU cc_start: 0.8520 (pm20) cc_final: 0.8267 (pm20) REVERT: R 252 ARG cc_start: 0.6763 (tpt90) cc_final: 0.6456 (tpt170) REVERT: R 338 ARG cc_start: 0.7157 (tpt170) cc_final: 0.6732 (tpt170) outliers start: 13 outliers final: 3 residues processed: 144 average time/residue: 1.6975 time to fit residues: 257.2277 Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.0570 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN R 363 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9144 Z= 0.156 Angle : 0.494 6.730 12376 Z= 0.270 Chirality : 0.041 0.136 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.247 20.507 1244 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.95 % Allowed : 13.67 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.72 (0.25), residues: 1124 helix: 2.69 (0.24), residues: 445 sheet: 0.75 (0.33), residues: 230 loop : -0.23 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 256 HIS 0.009 0.001 HIS A 357 PHE 0.014 0.001 PHE R 382 TYR 0.020 0.001 TYR R 146 ARG 0.006 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 1.023 Fit side-chains REVERT: A 17 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7552 (ptmm) REVERT: A 59 GLN cc_start: 0.8172 (tp40) cc_final: 0.7624 (mm-40) REVERT: A 314 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: G 17 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7761 (mm-30) REVERT: G 20 LYS cc_start: 0.8594 (mtmt) cc_final: 0.8159 (mtmt) REVERT: N 89 GLU cc_start: 0.8521 (pm20) cc_final: 0.8312 (pm20) REVERT: R 252 ARG cc_start: 0.6789 (tpt90) cc_final: 0.6443 (tpt170) REVERT: R 338 ARG cc_start: 0.7043 (tpt170) cc_final: 0.6595 (tpp-160) outliers start: 9 outliers final: 2 residues processed: 144 average time/residue: 1.6680 time to fit residues: 253.0524 Evaluate side-chains 142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 0.3980 chunk 59 optimal weight: 0.0010 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN N 84 ASN R 363 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9144 Z= 0.143 Angle : 0.477 7.762 12376 Z= 0.260 Chirality : 0.040 0.130 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.059 19.379 1244 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.95 % Allowed : 13.98 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.84 (0.25), residues: 1124 helix: 2.89 (0.24), residues: 439 sheet: 0.83 (0.33), residues: 228 loop : -0.23 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 256 HIS 0.008 0.001 HIS A 357 PHE 0.013 0.001 PHE R 382 TYR 0.020 0.001 TYR R 146 ARG 0.005 0.000 ARG R 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 1.100 Fit side-chains REVERT: A 17 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7556 (ptmm) REVERT: A 59 GLN cc_start: 0.8161 (tp40) cc_final: 0.7616 (mm-40) REVERT: A 314 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: G 17 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7780 (mm-30) REVERT: G 20 LYS cc_start: 0.8614 (mtmt) cc_final: 0.8167 (mtmt) REVERT: N 89 GLU cc_start: 0.8488 (pm20) cc_final: 0.8266 (pm20) REVERT: R 252 ARG cc_start: 0.6814 (tpt90) cc_final: 0.6447 (tpt170) REVERT: R 338 ARG cc_start: 0.7002 (tpt170) cc_final: 0.6656 (tpt170) outliers start: 9 outliers final: 2 residues processed: 150 average time/residue: 1.6254 time to fit residues: 257.1843 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN R 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9144 Z= 0.180 Angle : 0.507 8.569 12376 Z= 0.275 Chirality : 0.041 0.133 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.125 20.104 1244 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.95 % Allowed : 14.83 % Favored : 84.22 % 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: 1.76 (0.25), residues: 1124 helix: 2.76 (0.24), residues: 445 sheet: 0.84 (0.33), residues: 228 loop : -0.29 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 256 HIS 0.010 0.001 HIS A 357 PHE 0.023 0.001 PHE R 382 TYR 0.020 0.001 TYR R 146 ARG 0.008 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 1.070 Fit side-chains REVERT: A 17 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7537 (ptmm) REVERT: A 59 GLN cc_start: 0.8191 (tp40) cc_final: 0.7636 (mm-40) REVERT: A 314 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: G 17 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7703 (mm-30) REVERT: G 20 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8159 (mtmt) REVERT: R 252 ARG cc_start: 0.6756 (tpt90) cc_final: 0.6428 (tpt170) REVERT: R 338 ARG cc_start: 0.7040 (tpt170) cc_final: 0.6707 (tpt170) outliers start: 9 outliers final: 2 residues processed: 146 average time/residue: 1.6576 time to fit residues: 254.4165 Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 105 optimal weight: 0.0370 chunk 64 optimal weight: 1.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9144 Z= 0.180 Angle : 0.508 10.250 12376 Z= 0.276 Chirality : 0.041 0.134 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.158 19.978 1244 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.64 % Allowed : 15.25 % Favored : 84.11 % 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: 1.75 (0.25), residues: 1124 helix: 2.77 (0.24), residues: 445 sheet: 0.84 (0.33), residues: 228 loop : -0.32 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 256 HIS 0.010 0.001 HIS A 357 PHE 0.023 0.001 PHE R 382 TYR 0.020 0.001 TYR R 146 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 1.033 Fit side-chains REVERT: A 17 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7543 (ptmm) REVERT: A 59 GLN cc_start: 0.8192 (tp40) cc_final: 0.7634 (mm-40) REVERT: A 314 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: G 17 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7693 (mm-30) REVERT: G 20 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8136 (mtmt) REVERT: R 252 ARG cc_start: 0.6770 (tpt90) cc_final: 0.6436 (tpt170) REVERT: R 338 ARG cc_start: 0.7054 (tpt170) cc_final: 0.6724 (tpt170) outliers start: 6 outliers final: 2 residues processed: 142 average time/residue: 1.6837 time to fit residues: 251.2679 Evaluate side-chains 140 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 237 ASN N 82 GLN N 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9144 Z= 0.173 Angle : 0.514 10.276 12376 Z= 0.279 Chirality : 0.041 0.135 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.145 19.874 1244 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.53 % Allowed : 15.89 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.75 (0.25), residues: 1124 helix: 2.78 (0.24), residues: 445 sheet: 0.86 (0.33), residues: 228 loop : -0.33 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 256 HIS 0.010 0.001 HIS A 357 PHE 0.023 0.001 PHE R 382 TYR 0.020 0.001 TYR R 146 ARG 0.010 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 1.048 Fit side-chains REVERT: A 17 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7535 (ptmm) REVERT: A 59 GLN cc_start: 0.8150 (tp40) cc_final: 0.7601 (mm-40) REVERT: A 314 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: G 17 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7741 (mm-30) REVERT: G 20 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8138 (mtmt) REVERT: R 252 ARG cc_start: 0.6764 (tpt90) cc_final: 0.6428 (tpt170) REVERT: R 338 ARG cc_start: 0.7020 (tpt170) cc_final: 0.6693 (tpt170) outliers start: 5 outliers final: 2 residues processed: 143 average time/residue: 1.6790 time to fit residues: 253.4343 Evaluate side-chains 142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 5 optimal weight: 0.2980 chunk 63 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.142399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.089016 restraints weight = 22499.727| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.45 r_work: 0.2837 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9144 Z= 0.202 Angle : 0.545 10.076 12376 Z= 0.293 Chirality : 0.042 0.136 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.247 20.103 1244 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.64 % Allowed : 16.10 % Favored : 83.26 % 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: 1.74 (0.25), residues: 1124 helix: 2.75 (0.24), residues: 445 sheet: 0.82 (0.33), residues: 231 loop : -0.32 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP R 256 HIS 0.011 0.001 HIS A 357 PHE 0.022 0.001 PHE R 382 TYR 0.020 0.001 TYR R 146 ARG 0.010 0.001 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4320.10 seconds wall clock time: 77 minutes 55.69 seconds (4675.69 seconds total)