Starting phenix.real_space_refine on Sat Aug 23 00:55:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e3y_27873/08_2025/8e3y_27873.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e3y_27873/08_2025/8e3y_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_27873/08_2025/8e3y_27873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e3y_27873/08_2025/8e3y_27873.map" model { file = "/net/cci-nas-00/data/ceres_data/8e3y_27873/08_2025/8e3y_27873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e3y_27873/08_2025/8e3y_27873.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} 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: 2.10, per 1000 atoms: 0.23 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: 0.90 Conformation dependent library (CDL) restraints added in 347.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.32 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: 1.25 Time building geometry restraints manager: 1.17 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: 1.900 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.780 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.730 ------------------------------------------------------------------------------- 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 0.055 9149 Z= 0.222 Angle : 0.599 5.643 12386 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG B 197 TYR 0.011 0.001 TYR R 388 PHE 0.013 0.001 PHE A 212 TRP 0.011 0.001 TRP A 234 HIS 0.013 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9144) covalent geometry : angle 0.59874 (12376) SS BOND : bond 0.02467 ( 5) SS BOND : angle 1.13607 ( 10) hydrogen bonds : bond 0.13371 ( 461) hydrogen bonds : angle 5.73654 ( 1299) *********************** 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 : 0.271 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: 0.5922 time to fit residues: 103.5408 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 : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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 ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.140668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.089141 restraints weight = 16225.769| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.89 r_work: 0.2849 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9149 Z= 0.164 Angle : 0.552 8.624 12386 Z= 0.299 Chirality : 0.043 0.141 1369 Planarity : 0.004 0.051 1583 Dihedral : 4.259 22.270 1244 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.21 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.25), residues: 1124 helix: 2.61 (0.24), residues: 445 sheet: 0.67 (0.33), residues: 223 loop : -0.12 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 197 TYR 0.030 0.002 TYR R 146 PHE 0.014 0.002 PHE R 382 TRP 0.014 0.002 TRP B 339 HIS 0.022 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9144) covalent geometry : angle 0.55193 (12376) SS BOND : bond 0.00234 ( 5) SS BOND : angle 0.72601 ( 10) hydrogen bonds : bond 0.04641 ( 461) hydrogen bonds : angle 4.45433 ( 1299) *********************** 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 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7483 (ptmm) REVERT: A 59 GLN cc_start: 0.8389 (tp40) cc_final: 0.7601 (tm-30) REVERT: A 314 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: B 197 ARG cc_start: 0.8818 (mmm-85) cc_final: 0.8588 (mmm160) REVERT: B 266 HIS cc_start: 0.8635 (t-170) cc_final: 0.8420 (t-170) REVERT: B 270 ILE cc_start: 0.9204 (pt) cc_final: 0.8984 (pp) REVERT: G 17 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8185 (mm-30) REVERT: G 20 LYS cc_start: 0.8645 (mtmt) cc_final: 0.8366 (mtmt) REVERT: N 43 LYS cc_start: 0.8506 (mttm) cc_final: 0.8142 (mttp) REVERT: R 252 ARG cc_start: 0.7039 (tpt90) cc_final: 0.6610 (tpt170) outliers start: 11 outliers final: 3 residues processed: 149 average time/residue: 0.5999 time to fit residues: 94.2439 Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS 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 N 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.141227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.088315 restraints weight = 13050.576| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.27 r_work: 0.2865 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9149 Z= 0.152 Angle : 0.529 7.695 12386 Z= 0.289 Chirality : 0.043 0.136 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.347 21.731 1244 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.27 % Allowed : 10.70 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.25), residues: 1124 helix: 2.63 (0.24), residues: 445 sheet: 0.74 (0.33), residues: 231 loop : -0.20 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.025 0.001 TYR R 146 PHE 0.014 0.002 PHE R 382 TRP 0.017 0.002 TRP R 256 HIS 0.019 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9144) covalent geometry : angle 0.52871 (12376) SS BOND : bond 0.00372 ( 5) SS BOND : angle 0.67985 ( 10) hydrogen bonds : bond 0.04550 ( 461) hydrogen bonds : angle 4.35142 ( 1299) *********************** 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 159 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7585 (ptmm) REVERT: A 20 ARG cc_start: 0.7937 (mtm-85) cc_final: 0.7699 (mtm-85) REVERT: A 59 GLN cc_start: 0.8369 (tp40) cc_final: 0.7759 (mm-40) REVERT: A 314 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: B 270 ILE cc_start: 0.9254 (pt) cc_final: 0.9051 (pp) REVERT: G 20 LYS cc_start: 0.8659 (mtmt) cc_final: 0.8418 (mtmt) REVERT: N 43 LYS cc_start: 0.8594 (mttm) cc_final: 0.8249 (mttp) REVERT: N 89 GLU cc_start: 0.8667 (pm20) cc_final: 0.8434 (pm20) REVERT: R 252 ARG cc_start: 0.6997 (tpt90) cc_final: 0.6559 (tpt170) REVERT: R 338 ARG cc_start: 0.6977 (tpt170) cc_final: 0.6623 (tpt170) outliers start: 12 outliers final: 2 residues processed: 150 average time/residue: 0.6622 time to fit residues: 104.3963 Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 70 optimal weight: 0.2980 chunk 76 optimal weight: 30.0000 chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.086495 restraints weight = 22663.471| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.46 r_work: 0.2806 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9149 Z= 0.144 Angle : 0.515 7.248 12386 Z= 0.282 Chirality : 0.042 0.136 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.328 20.919 1244 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.17 % Allowed : 11.33 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.25), residues: 1124 helix: 2.63 (0.24), residues: 445 sheet: 0.76 (0.33), residues: 231 loop : -0.19 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.024 0.001 TYR R 146 PHE 0.013 0.001 PHE R 222 TRP 0.020 0.002 TRP R 256 HIS 0.016 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9144) covalent geometry : angle 0.51537 (12376) SS BOND : bond 0.00232 ( 5) SS BOND : angle 0.64359 ( 10) hydrogen bonds : bond 0.04400 ( 461) hydrogen bonds : angle 4.30341 ( 1299) *********************** 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 154 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.382 Fit side-chains REVERT: A 17 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7543 (ptmm) REVERT: A 59 GLN cc_start: 0.8308 (tp40) cc_final: 0.7703 (mm-40) REVERT: B 197 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8314 (mmm160) REVERT: B 270 ILE cc_start: 0.9210 (pt) cc_final: 0.8997 (pp) REVERT: G 17 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8101 (mm-30) REVERT: G 20 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8298 (mtmt) REVERT: N 43 LYS cc_start: 0.8564 (mttm) cc_final: 0.8333 (mttp) REVERT: R 252 ARG cc_start: 0.6986 (tpt90) cc_final: 0.6539 (tpt170) REVERT: R 338 ARG cc_start: 0.6922 (tpt170) cc_final: 0.6567 (tpt170) outliers start: 11 outliers final: 2 residues processed: 145 average time/residue: 0.6633 time to fit residues: 101.2451 Evaluate side-chains 146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS 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 104 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 84 ASN N 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.139141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.085377 restraints weight = 21043.702| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.34 r_work: 0.2802 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9149 Z= 0.165 Angle : 0.542 7.721 12386 Z= 0.296 Chirality : 0.043 0.137 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.432 21.201 1244 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.17 % Allowed : 12.18 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.25), residues: 1124 helix: 2.62 (0.24), residues: 445 sheet: 0.84 (0.33), residues: 229 loop : -0.23 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 20 TYR 0.023 0.001 TYR R 146 PHE 0.015 0.002 PHE R 222 TRP 0.018 0.002 TRP R 256 HIS 0.016 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9144) covalent geometry : angle 0.54150 (12376) SS BOND : bond 0.00216 ( 5) SS BOND : angle 0.71139 ( 10) hydrogen bonds : bond 0.04610 ( 461) hydrogen bonds : angle 4.34790 ( 1299) *********************** 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 151 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7584 (ptmm) REVERT: A 59 GLN cc_start: 0.8357 (tp40) cc_final: 0.7779 (mm-40) REVERT: B 59 TYR cc_start: 0.9419 (OUTLIER) cc_final: 0.9213 (m-80) REVERT: B 266 HIS cc_start: 0.8571 (t-170) cc_final: 0.8332 (t-170) REVERT: B 270 ILE cc_start: 0.9250 (pt) cc_final: 0.9036 (pp) REVERT: G 17 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8201 (mm-30) REVERT: G 20 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8361 (mtmt) REVERT: N 43 LYS cc_start: 0.8663 (mttm) cc_final: 0.8430 (mttp) REVERT: N 89 GLU cc_start: 0.8752 (pm20) cc_final: 0.8453 (pm20) REVERT: R 252 ARG cc_start: 0.6970 (tpt90) cc_final: 0.6495 (tpt170) REVERT: R 338 ARG cc_start: 0.7056 (tpt170) cc_final: 0.6599 (tpp-160) outliers start: 11 outliers final: 3 residues processed: 143 average time/residue: 0.6184 time to fit residues: 93.1303 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 : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 59 TYR 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 43 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 30 optimal weight: 0.0670 chunk 10 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS N 3 GLN N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.088259 restraints weight = 21524.064| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.04 r_work: 0.2834 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9149 Z= 0.121 Angle : 0.496 8.123 12386 Z= 0.270 Chirality : 0.041 0.135 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.238 20.109 1244 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.85 % Allowed : 13.45 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.25), residues: 1124 helix: 2.72 (0.24), residues: 445 sheet: 0.78 (0.33), residues: 231 loop : -0.21 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 20 TYR 0.021 0.001 TYR R 146 PHE 0.012 0.001 PHE R 382 TRP 0.021 0.002 TRP R 256 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9144) covalent geometry : angle 0.49556 (12376) SS BOND : bond 0.00205 ( 5) SS BOND : angle 0.59324 ( 10) hydrogen bonds : bond 0.04101 ( 461) hydrogen bonds : angle 4.19480 ( 1299) *********************** 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 154 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.366 Fit side-chains REVERT: A 17 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7588 (ptmm) REVERT: A 59 GLN cc_start: 0.8244 (tp40) cc_final: 0.7644 (mm-40) REVERT: B 266 HIS cc_start: 0.8460 (t-170) cc_final: 0.8228 (t-170) REVERT: B 270 ILE cc_start: 0.9200 (pt) cc_final: 0.8985 (pp) REVERT: G 17 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8051 (mm-30) REVERT: G 20 LYS cc_start: 0.8669 (mtmt) cc_final: 0.8295 (mtmt) REVERT: G 21 MET cc_start: 0.8444 (tpp) cc_final: 0.7965 (tmt) REVERT: N 43 LYS cc_start: 0.8586 (mttm) cc_final: 0.8364 (mttp) REVERT: R 252 ARG cc_start: 0.6973 (tpt90) cc_final: 0.6523 (tpt170) REVERT: R 338 ARG cc_start: 0.6923 (tpt170) cc_final: 0.6588 (tpt170) outliers start: 8 outliers final: 2 residues processed: 147 average time/residue: 0.6853 time to fit residues: 105.6308 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS 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 9 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 74 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 84 ASN R 178 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.141675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.089258 restraints weight = 21544.243| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.05 r_work: 0.2823 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9149 Z= 0.133 Angle : 0.512 8.813 12386 Z= 0.279 Chirality : 0.042 0.134 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.302 21.965 1244 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.06 % Allowed : 13.98 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.25), residues: 1124 helix: 2.71 (0.24), residues: 445 sheet: 0.84 (0.33), residues: 229 loop : -0.25 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 400 TYR 0.021 0.001 TYR R 146 PHE 0.023 0.001 PHE R 382 TRP 0.026 0.002 TRP R 256 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9144) covalent geometry : angle 0.51168 (12376) SS BOND : bond 0.00275 ( 5) SS BOND : angle 0.69949 ( 10) hydrogen bonds : bond 0.04187 ( 461) hydrogen bonds : angle 4.20163 ( 1299) *********************** 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 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.264 Fit side-chains REVERT: A 17 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7547 (ptmm) REVERT: A 59 GLN cc_start: 0.8291 (tp40) cc_final: 0.7685 (mm-40) REVERT: B 197 ARG cc_start: 0.8811 (mmm160) cc_final: 0.8558 (mtp180) REVERT: B 266 HIS cc_start: 0.8562 (t-170) cc_final: 0.8338 (t-170) REVERT: B 270 ILE cc_start: 0.9232 (pt) cc_final: 0.9006 (pp) REVERT: G 17 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8128 (mm-30) REVERT: G 20 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8329 (mtmt) REVERT: G 21 MET cc_start: 0.8601 (tpp) cc_final: 0.8010 (tmt) REVERT: N 43 LYS cc_start: 0.8611 (mttm) cc_final: 0.8387 (mttp) REVERT: R 252 ARG cc_start: 0.6956 (tpt90) cc_final: 0.6460 (tpt170) REVERT: R 338 ARG cc_start: 0.6981 (tpt170) cc_final: 0.6627 (tpt170) outliers start: 10 outliers final: 2 residues processed: 145 average time/residue: 0.6552 time to fit residues: 100.1081 Evaluate side-chains 142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 139 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS 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 97 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.142641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.090459 restraints weight = 21384.964| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 3.28 r_work: 0.2846 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9149 Z= 0.115 Angle : 0.502 9.159 12386 Z= 0.273 Chirality : 0.041 0.134 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.204 19.833 1244 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.74 % Allowed : 14.94 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.25), residues: 1124 helix: 2.77 (0.24), residues: 445 sheet: 0.81 (0.33), residues: 228 loop : -0.27 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.020 0.001 TYR R 146 PHE 0.023 0.001 PHE R 382 TRP 0.028 0.002 TRP R 256 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9144) covalent geometry : angle 0.50192 (12376) SS BOND : bond 0.00317 ( 5) SS BOND : angle 0.65766 ( 10) hydrogen bonds : bond 0.03946 ( 461) hydrogen bonds : angle 4.11695 ( 1299) *********************** 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 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.253 Fit side-chains REVERT: A 17 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7615 (ptmm) REVERT: A 59 GLN cc_start: 0.8243 (tp40) cc_final: 0.7634 (mm-40) REVERT: B 197 ARG cc_start: 0.8568 (mmm160) cc_final: 0.8362 (mtp180) REVERT: B 266 HIS cc_start: 0.8457 (t-170) cc_final: 0.8243 (t-170) REVERT: G 17 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8068 (mm-30) REVERT: G 20 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8346 (mtmt) REVERT: G 21 MET cc_start: 0.8518 (tpp) cc_final: 0.7988 (tmt) REVERT: N 43 LYS cc_start: 0.8557 (mttm) cc_final: 0.8345 (mttp) REVERT: N 87 LYS cc_start: 0.8507 (mtmm) cc_final: 0.8019 (mtpt) REVERT: R 252 ARG cc_start: 0.6950 (tpt90) cc_final: 0.6491 (tpt170) REVERT: R 338 ARG cc_start: 0.6889 (tpt170) cc_final: 0.6551 (tpt170) outliers start: 7 outliers final: 2 residues processed: 147 average time/residue: 0.6325 time to fit residues: 97.7224 Evaluate side-chains 141 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS 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 4 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.0000 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.143851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.090774 restraints weight = 20686.744| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.23 r_work: 0.2872 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9149 Z= 0.105 Angle : 0.493 8.951 12386 Z= 0.268 Chirality : 0.041 0.132 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.062 19.243 1244 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.42 % Allowed : 15.15 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.25), residues: 1124 helix: 2.94 (0.24), residues: 439 sheet: 0.83 (0.33), residues: 228 loop : -0.24 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.020 0.001 TYR R 146 PHE 0.024 0.001 PHE R 382 TRP 0.034 0.002 TRP R 256 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9144) covalent geometry : angle 0.49320 (12376) SS BOND : bond 0.00246 ( 5) SS BOND : angle 0.53135 ( 10) hydrogen bonds : bond 0.03731 ( 461) hydrogen bonds : angle 4.04655 ( 1299) *********************** 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 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.218 Fit side-chains REVERT: A 17 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7572 (ptmm) REVERT: A 59 GLN cc_start: 0.8252 (tp40) cc_final: 0.7632 (mm-40) REVERT: B 266 HIS cc_start: 0.8466 (t-170) cc_final: 0.8262 (t-170) REVERT: G 17 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8047 (mm-30) REVERT: G 20 LYS cc_start: 0.8685 (mtmt) cc_final: 0.8303 (mtmt) REVERT: G 21 MET cc_start: 0.8486 (tpp) cc_final: 0.7946 (tmt) REVERT: N 43 LYS cc_start: 0.8551 (mttm) cc_final: 0.8339 (mttp) REVERT: R 252 ARG cc_start: 0.7000 (tpt90) cc_final: 0.6449 (tpt90) REVERT: R 338 ARG cc_start: 0.6867 (tpt170) cc_final: 0.6511 (tpt170) outliers start: 4 outliers final: 2 residues processed: 143 average time/residue: 0.6583 time to fit residues: 99.2185 Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS 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 102 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 61 optimal weight: 0.0370 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.142237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.090773 restraints weight = 16505.987| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.73 r_work: 0.2862 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9149 Z= 0.131 Angle : 0.524 8.774 12386 Z= 0.285 Chirality : 0.042 0.135 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.201 20.203 1244 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.42 % Allowed : 15.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.25), residues: 1124 helix: 2.80 (0.24), residues: 445 sheet: 0.83 (0.33), residues: 229 loop : -0.29 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 400 TYR 0.020 0.001 TYR R 146 PHE 0.022 0.001 PHE R 382 TRP 0.043 0.002 TRP R 256 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9144) covalent geometry : angle 0.52421 (12376) SS BOND : bond 0.00311 ( 5) SS BOND : angle 0.63380 ( 10) hydrogen bonds : bond 0.04076 ( 461) hydrogen bonds : angle 4.14274 ( 1299) ********************** 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 147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 143 time to evaluate : 0.368 Fit side-chains REVERT: A 17 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7550 (ptmm) REVERT: A 59 GLN cc_start: 0.8317 (tp40) cc_final: 0.7706 (mm-40) REVERT: G 17 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8124 (mm-30) REVERT: G 20 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8383 (mtmt) REVERT: G 21 MET cc_start: 0.8587 (tpp) cc_final: 0.7976 (tmt) REVERT: N 43 LYS cc_start: 0.8604 (mttm) cc_final: 0.8379 (mttp) REVERT: R 252 ARG cc_start: 0.6971 (tpt90) cc_final: 0.6457 (tpt170) REVERT: R 338 ARG cc_start: 0.6972 (tpt170) cc_final: 0.6594 (tpt170) outliers start: 4 outliers final: 2 residues processed: 144 average time/residue: 0.7018 time to fit residues: 106.2188 Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS 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 52 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS 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 3 GLN ** P 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.142743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.089903 restraints weight = 14363.887| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.39 r_work: 0.2890 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9149 Z= 0.116 Angle : 0.516 8.660 12386 Z= 0.281 Chirality : 0.041 0.134 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.150 19.649 1244 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.53 % Allowed : 15.47 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.25), residues: 1124 helix: 2.88 (0.24), residues: 444 sheet: 0.73 (0.33), residues: 230 loop : -0.22 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 96 TYR 0.020 0.001 TYR R 146 PHE 0.023 0.001 PHE R 382 TRP 0.046 0.002 TRP R 256 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9144) covalent geometry : angle 0.51636 (12376) SS BOND : bond 0.00275 ( 5) SS BOND : angle 0.55670 ( 10) hydrogen bonds : bond 0.03893 ( 461) hydrogen bonds : angle 4.10215 ( 1299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5030.80 seconds wall clock time: 85 minutes 54.68 seconds (5154.68 seconds total)