Starting phenix.real_space_refine on Tue Jan 14 14:48:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fhb_50444/01_2025/9fhb_50444.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fhb_50444/01_2025/9fhb_50444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fhb_50444/01_2025/9fhb_50444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fhb_50444/01_2025/9fhb_50444.map" model { file = "/net/cci-nas-00/data/ceres_data/9fhb_50444/01_2025/9fhb_50444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fhb_50444/01_2025/9fhb_50444.cif" } resolution = 3.87 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= 0.050 sd= 0.131 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 2 7.16 5 S 42 5.16 5 C 4268 2.51 5 N 1171 2.21 5 O 1266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6751 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1123 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "C" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1982 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 12, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2447 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 3, 'TRANS': 317} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.72, per 1000 atoms: 0.70 Number of scatterers: 6751 At special positions: 0 Unit cell: (86.92, 98.58, 108.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 Ca 2 19.99 S 42 16.00 O 1266 8.00 N 1171 7.00 C 4268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 266 " distance=2.05 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 351 " - pdb=" SG CYS C 381 " distance=2.03 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 202 " distance=2.02 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 197 " - pdb=" SG CYS D 258 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 238 " distance=2.03 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 355 " distance=2.04 Simple disulfide: pdb=" SG CYS D 304 " - pdb=" SG CYS D 365 " distance=2.03 Simple disulfide: pdb=" SG CYS D 335 " - pdb=" SG CYS D 345 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 416 " distance=2.02 Simple disulfide: pdb=" SG CYS D 398 " - pdb=" SG CYS D 462 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 472 " distance=2.04 Simple disulfide: pdb=" SG CYS D 442 " - pdb=" SG CYS D 452 " 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=3, symmetry=0 Links applied NAG-ASN " NAG C1001 " - " ASN C 184 " " NAG C1002 " - " ASN C 241 " " NAG D2003 " - " ASN D 320 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 998.5 milliseconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 39.8% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.573A pdb=" N THR A 41 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 95 through 113 removed outlier: 3.738A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 137 Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 36 through 46 removed outlier: 4.134A pdb=" N GLU B 43 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N SER B 44 " --> pdb=" O PHE B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 57 through 76 Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.508A pdb=" N THR B 84 " --> pdb=" O ASN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 95 removed outlier: 3.562A pdb=" N LYS B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 119 removed outlier: 3.857A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 142 Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 213 through 218 Processing helix chain 'C' and resid 305 through 314 Processing helix chain 'C' and resid 318 through 322 Processing helix chain 'C' and resid 395 through 405 Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 249 through 253 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 296 through 308 Processing helix chain 'D' and resid 341 through 345 Processing helix chain 'D' and resid 403 through 414 Processing helix chain 'D' and resid 448 through 452 Processing sheet with id=AA1, first strand: chain 'C' and resid 229 through 230 Processing sheet with id=AA2, first strand: chain 'C' and resid 278 through 283 removed outlier: 4.742A pdb=" N CYS C 340 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C 388 " --> pdb=" O SER C 376 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N TRP C 369 " --> pdb=" O ASP C 363 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP C 363 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ALA C 371 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 361 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 373 " --> pdb=" O PHE C 359 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA C 358 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER C 282 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS C 362 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N VAL C 278 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 158 through 166 removed outlier: 3.633A pdb=" N GLU D 158 " --> pdb=" O LYS D 175 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER D 169 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER D 207 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 158 through 166 removed outlier: 3.633A pdb=" N GLU D 158 " --> pdb=" O LYS D 175 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER D 169 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE D 172 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL D 183 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N TRP D 222 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N THR D 182 " --> pdb=" O TRP D 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 264 through 269 Processing sheet with id=AA6, first strand: chain 'D' and resid 264 through 269 removed outlier: 7.038A pdb=" N LEU D 279 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE D 290 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N TRP D 329 " --> pdb=" O TRP D 287 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N THR D 289 " --> pdb=" O TRP D 329 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 372 through 380 removed outlier: 4.934A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 372 through 380 removed outlier: 4.934A pdb=" N ALA D 383 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL D 386 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL D 397 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LEU D 437 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS D 396 " --> pdb=" O LEU D 437 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 879 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: 2.07 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 2796 1.39 - 1.55: 4066 1.55 - 1.72: 1 1.72 - 1.89: 51 1.89 - 2.05: 8 Bond restraints: 6922 Sorted by residual: bond pdb=" CB CYS C 149 " pdb=" SG CYS C 149 " ideal model delta sigma weight residual 1.808 1.874 -0.066 3.30e-02 9.18e+02 3.96e+00 bond pdb=" CB CYS C 266 " pdb=" SG CYS C 266 " ideal model delta sigma weight residual 1.808 1.748 0.060 3.30e-02 9.18e+02 3.25e+00 bond pdb=" CA ASP A 75 " pdb=" C ASP A 75 " ideal model delta sigma weight residual 1.522 1.547 -0.026 1.52e-02 4.33e+03 2.81e+00 bond pdb=" CB VAL B 54 " pdb=" CG2 VAL B 54 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.49e+00 bond pdb=" CG ASP A 75 " pdb=" OD1 ASP A 75 " ideal model delta sigma weight residual 1.249 1.220 0.029 1.90e-02 2.77e+03 2.31e+00 ... (remaining 6917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 9034 2.19 - 4.38: 319 4.38 - 6.57: 50 6.57 - 8.76: 14 8.76 - 10.95: 2 Bond angle restraints: 9419 Sorted by residual: angle pdb=" N ASP A 75 " pdb=" CA ASP A 75 " pdb=" C ASP A 75 " ideal model delta sigma weight residual 110.61 103.76 6.85 1.25e+00 6.40e-01 3.00e+01 angle pdb=" CA ASP A 75 " pdb=" C ASP A 75 " pdb=" O ASP A 75 " ideal model delta sigma weight residual 121.20 126.75 -5.55 1.04e+00 9.25e-01 2.85e+01 angle pdb=" N LYS C 379 " pdb=" CA LYS C 379 " pdb=" C LYS C 379 " ideal model delta sigma weight residual 113.61 106.28 7.33 1.50e+00 4.44e-01 2.39e+01 angle pdb=" CA CYS C 266 " pdb=" CB CYS C 266 " pdb=" SG CYS C 266 " ideal model delta sigma weight residual 114.40 125.35 -10.95 2.30e+00 1.89e-01 2.27e+01 angle pdb=" C CYS C 266 " pdb=" CA CYS C 266 " pdb=" CB CYS C 266 " ideal model delta sigma weight residual 109.46 117.17 -7.71 1.84e+00 2.95e-01 1.75e+01 ... (remaining 9414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 3773 22.84 - 45.67: 241 45.67 - 68.51: 46 68.51 - 91.35: 17 91.35 - 114.18: 1 Dihedral angle restraints: 4078 sinusoidal: 1633 harmonic: 2445 Sorted by residual: dihedral pdb=" CB CYS D 411 " pdb=" SG CYS D 411 " pdb=" SG CYS D 472 " pdb=" CB CYS D 472 " ideal model delta sinusoidal sigma weight residual 93.00 163.09 -70.09 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CB CYS C 149 " pdb=" SG CYS C 149 " pdb=" SG CYS C 266 " pdb=" CB CYS C 266 " ideal model delta sinusoidal sigma weight residual -86.00 -15.96 -70.04 1 1.00e+01 1.00e-02 6.32e+01 dihedral pdb=" CB CYS D 291 " pdb=" SG CYS D 291 " pdb=" SG CYS D 355 " pdb=" CB CYS D 355 " ideal model delta sinusoidal sigma weight residual 93.00 28.74 64.26 1 1.00e+01 1.00e-02 5.43e+01 ... (remaining 4075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 664 0.043 - 0.085: 240 0.085 - 0.128: 89 0.128 - 0.170: 19 0.170 - 0.213: 11 Chirality restraints: 1023 Sorted by residual: chirality pdb=" CA CYS D 382 " pdb=" N CYS D 382 " pdb=" C CYS D 382 " pdb=" CB CYS D 382 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA PRO B 5 " pdb=" N PRO B 5 " pdb=" C PRO B 5 " pdb=" CB PRO B 5 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CG LEU D 264 " pdb=" CB LEU D 264 " pdb=" CD1 LEU D 264 " pdb=" CD2 LEU D 264 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1020 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 35 " 0.030 2.00e-02 2.50e+03 3.72e-02 2.77e+01 pdb=" CG TYR B 35 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 TYR B 35 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 35 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR B 35 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR B 35 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 35 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 35 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 47 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C ASP B 47 " 0.055 2.00e-02 2.50e+03 pdb=" O ASP B 47 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 48 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 198 " 0.186 9.50e-02 1.11e+02 8.41e-02 5.71e+00 pdb=" NE ARG D 198 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG D 198 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG D 198 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG D 198 " -0.000 2.00e-02 2.50e+03 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 213 2.69 - 3.24: 6717 3.24 - 3.80: 10782 3.80 - 4.35: 13593 4.35 - 4.90: 22418 Nonbonded interactions: 53723 Sorted by model distance: nonbonded pdb=" OD1 ASP D 249 " pdb=" N HIS D 250 " model vdw 2.140 3.120 nonbonded pdb=" O GLY D 164 " pdb=" OG SER D 169 " model vdw 2.147 3.040 nonbonded pdb=" ND2 ASN D 247 " pdb="CA CA D2001 " model vdw 2.154 2.590 nonbonded pdb=" OD1 ASP C 349 " pdb=" N THR C 350 " model vdw 2.203 3.120 nonbonded pdb=" N ASP B 99 " pdb=" OD1 ASP B 99 " model vdw 2.225 3.120 ... (remaining 53718 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.040 Find NCS groups from input model: 0.060 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 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 : 0.005 0.066 6922 Z= 0.311 Angle : 0.956 10.954 9419 Z= 0.528 Chirality : 0.054 0.213 1023 Planarity : 0.006 0.084 1200 Dihedral : 15.857 114.181 2467 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.82 % Allowed : 4.11 % Favored : 95.07 % Rotamer: Outliers : 3.25 % Allowed : 17.51 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 852 helix: 0.50 (0.27), residues: 289 sheet: -1.05 (0.48), residues: 92 loop : -0.54 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP D 455 HIS 0.009 0.001 HIS A 122 PHE 0.016 0.002 PHE D 438 TYR 0.092 0.003 TYR B 35 ARG 0.021 0.002 ARG D 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 GLU cc_start: 0.8062 (tp30) cc_final: 0.7457 (tp30) REVERT: B 94 ASP cc_start: 0.6962 (t70) cc_final: 0.6367 (m-30) REVERT: B 122 PHE cc_start: 0.8255 (t80) cc_final: 0.8001 (t80) REVERT: C 242 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6411 (m-80) REVERT: C 314 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: C 354 ASP cc_start: 0.7376 (m-30) cc_final: 0.6805 (m-30) REVERT: D 161 LEU cc_start: 0.8743 (mt) cc_final: 0.8332 (mt) REVERT: D 436 TRP cc_start: 0.8404 (m-90) cc_final: 0.8135 (m-10) outliers start: 23 outliers final: 16 residues processed: 146 average time/residue: 0.1669 time to fit residues: 33.5556 Evaluate side-chains 129 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 242 TYR Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 331 ASP Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 414 LEU Chi-restraints excluded: chain D residue 434 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.0770 chunk 34 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 HIS C 195 GLN C 208 HIS C 289 ASN ** D 199 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 = 0.3856 r_free = 0.3856 target = 0.140512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120202 restraints weight = 14167.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.123553 restraints weight = 8032.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.125719 restraints weight = 5386.315| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6922 Z= 0.228 Angle : 0.653 8.244 9419 Z= 0.331 Chirality : 0.045 0.160 1023 Planarity : 0.004 0.039 1200 Dihedral : 10.323 111.506 1013 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 4.66 % Allowed : 16.10 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.28), residues: 852 helix: 2.25 (0.31), residues: 281 sheet: -0.24 (0.51), residues: 86 loop : -0.18 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 455 HIS 0.005 0.001 HIS A 122 PHE 0.011 0.001 PHE C 359 TYR 0.025 0.002 TYR B 35 ARG 0.007 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 SER cc_start: 0.8920 (m) cc_final: 0.8368 (p) REVERT: B 35 TYR cc_start: 0.8102 (m-10) cc_final: 0.7420 (m-10) REVERT: C 242 TYR cc_start: 0.7108 (OUTLIER) cc_final: 0.6791 (m-80) REVERT: C 354 ASP cc_start: 0.7627 (m-30) cc_final: 0.7385 (m-30) REVERT: D 360 ASP cc_start: 0.8460 (m-30) cc_final: 0.7951 (m-30) REVERT: D 396 LYS cc_start: 0.8321 (pttt) cc_final: 0.7885 (pttt) REVERT: D 436 TRP cc_start: 0.8558 (m-90) cc_final: 0.8280 (m-10) outliers start: 33 outliers final: 18 residues processed: 139 average time/residue: 0.1700 time to fit residues: 33.2313 Evaluate side-chains 122 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 HIS Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 242 TYR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 373 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS B 117 HIS C 203 ASN C 208 HIS ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117533 restraints weight = 14353.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120856 restraints weight = 8146.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.123057 restraints weight = 5511.648| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6922 Z= 0.227 Angle : 0.606 8.120 9419 Z= 0.306 Chirality : 0.043 0.150 1023 Planarity : 0.004 0.046 1200 Dihedral : 9.655 109.134 997 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 4.38 % Allowed : 18.08 % Favored : 77.54 % 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: 1.04 (0.29), residues: 852 helix: 2.20 (0.32), residues: 284 sheet: -0.36 (0.54), residues: 75 loop : 0.01 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 37 HIS 0.003 0.001 HIS D 246 PHE 0.018 0.002 PHE A 36 TYR 0.015 0.002 TYR B 35 ARG 0.008 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 THR cc_start: 0.8751 (p) cc_final: 0.8516 (p) REVERT: B 35 TYR cc_start: 0.8355 (m-80) cc_final: 0.7735 (m-10) REVERT: C 242 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.6844 (m-80) REVERT: C 354 ASP cc_start: 0.7960 (m-30) cc_final: 0.7532 (m-30) REVERT: D 396 LYS cc_start: 0.8383 (pttt) cc_final: 0.8051 (pttt) REVERT: D 436 TRP cc_start: 0.8577 (m-90) cc_final: 0.8371 (m-10) outliers start: 31 outliers final: 19 residues processed: 134 average time/residue: 0.1559 time to fit residues: 29.6175 Evaluate side-chains 121 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 TYR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 50 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 HIS C 331 GLN ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.137619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.117179 restraints weight = 14602.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120527 restraints weight = 8313.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122720 restraints weight = 5639.800| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6922 Z= 0.211 Angle : 0.583 8.625 9419 Z= 0.294 Chirality : 0.043 0.148 1023 Planarity : 0.004 0.045 1200 Dihedral : 9.358 106.387 991 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.40 % Favored : 96.48 % Rotamer: Outliers : 4.10 % Allowed : 19.07 % Favored : 76.84 % 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: 1.03 (0.29), residues: 852 helix: 1.98 (0.32), residues: 292 sheet: -0.34 (0.53), residues: 75 loop : 0.12 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 37 HIS 0.003 0.001 HIS D 246 PHE 0.019 0.001 PHE A 36 TYR 0.012 0.001 TYR B 35 ARG 0.008 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 THR cc_start: 0.8773 (p) cc_final: 0.8400 (p) REVERT: B 35 TYR cc_start: 0.8377 (m-80) cc_final: 0.7797 (m-10) REVERT: D 176 PHE cc_start: 0.7351 (t80) cc_final: 0.6530 (m-80) REVERT: D 223 PHE cc_start: 0.7953 (m-80) cc_final: 0.7550 (m-80) REVERT: D 328 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8067 (mm) REVERT: D 396 LYS cc_start: 0.8373 (pttt) cc_final: 0.8094 (pttt) outliers start: 29 outliers final: 19 residues processed: 129 average time/residue: 0.1625 time to fit residues: 29.2204 Evaluate side-chains 124 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 22 optimal weight: 0.7980 chunk 46 optimal weight: 0.0980 chunk 60 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.137514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.117354 restraints weight = 14366.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120677 restraints weight = 8316.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.122823 restraints weight = 5672.538| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6922 Z= 0.200 Angle : 0.582 7.645 9419 Z= 0.292 Chirality : 0.042 0.146 1023 Planarity : 0.004 0.048 1200 Dihedral : 9.148 104.242 989 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 4.10 % Allowed : 19.49 % Favored : 76.41 % 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: 1.07 (0.29), residues: 852 helix: 1.96 (0.32), residues: 292 sheet: -0.27 (0.58), residues: 63 loop : 0.15 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 398 HIS 0.004 0.001 HIS D 246 PHE 0.020 0.002 PHE A 36 TYR 0.010 0.001 TYR B 35 ARG 0.006 0.001 ARG D 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 THR cc_start: 0.8724 (p) cc_final: 0.8472 (p) REVERT: B 35 TYR cc_start: 0.8372 (m-80) cc_final: 0.7838 (m-10) REVERT: B 90 GLU cc_start: 0.8217 (tp30) cc_final: 0.7276 (tp30) REVERT: B 94 ASP cc_start: 0.7353 (t70) cc_final: 0.6990 (m-30) REVERT: D 223 PHE cc_start: 0.7952 (m-80) cc_final: 0.7533 (m-80) REVERT: D 328 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8155 (mm) REVERT: D 396 LYS cc_start: 0.8287 (pttt) cc_final: 0.8060 (pttt) REVERT: D 436 TRP cc_start: 0.8523 (m-10) cc_final: 0.8222 (m-10) outliers start: 29 outliers final: 23 residues processed: 127 average time/residue: 0.1612 time to fit residues: 29.0039 Evaluate side-chains 119 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 18 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.134320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114075 restraints weight = 14516.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117334 restraints weight = 8426.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.119495 restraints weight = 5777.092| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 6922 Z= 0.261 Angle : 0.599 7.634 9419 Z= 0.302 Chirality : 0.043 0.151 1023 Planarity : 0.004 0.051 1200 Dihedral : 9.279 103.645 989 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.05 % Favored : 96.83 % Rotamer: Outliers : 4.52 % Allowed : 19.07 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.30), residues: 852 helix: 1.92 (0.32), residues: 292 sheet: -0.57 (0.53), residues: 83 loop : 0.15 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 37 HIS 0.005 0.001 HIS D 246 PHE 0.013 0.002 PHE A 36 TYR 0.012 0.002 TYR C 224 ARG 0.006 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 THR cc_start: 0.8741 (p) cc_final: 0.8481 (p) REVERT: B 35 TYR cc_start: 0.8457 (m-80) cc_final: 0.7964 (m-10) REVERT: B 80 ASN cc_start: 0.6884 (t0) cc_final: 0.6475 (t0) REVERT: B 90 GLU cc_start: 0.8263 (tp30) cc_final: 0.7418 (tp30) REVERT: B 94 ASP cc_start: 0.7431 (t70) cc_final: 0.6967 (m-30) REVERT: C 242 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: D 396 LYS cc_start: 0.8459 (pttt) cc_final: 0.8233 (pttt) outliers start: 32 outliers final: 26 residues processed: 124 average time/residue: 0.1749 time to fit residues: 30.5583 Evaluate side-chains 128 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 TYR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 373 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 11 optimal weight: 0.0970 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.137174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117337 restraints weight = 14364.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120580 restraints weight = 8356.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122773 restraints weight = 5744.373| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6922 Z= 0.188 Angle : 0.575 8.979 9419 Z= 0.287 Chirality : 0.042 0.147 1023 Planarity : 0.004 0.052 1200 Dihedral : 9.011 102.676 988 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.23 % Favored : 95.66 % Rotamer: Outliers : 3.95 % Allowed : 20.76 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.30), residues: 852 helix: 1.93 (0.32), residues: 292 sheet: -0.65 (0.53), residues: 83 loop : 0.17 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 398 HIS 0.005 0.001 HIS D 246 PHE 0.014 0.001 PHE A 36 TYR 0.010 0.001 TYR B 35 ARG 0.007 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 137 THR cc_start: 0.8759 (p) cc_final: 0.8489 (p) REVERT: B 90 GLU cc_start: 0.8212 (tp30) cc_final: 0.7389 (tp30) REVERT: B 94 ASP cc_start: 0.7418 (t70) cc_final: 0.7003 (m-30) REVERT: B 121 GLU cc_start: 0.8326 (tp30) cc_final: 0.8120 (tp30) outliers start: 28 outliers final: 27 residues processed: 125 average time/residue: 0.1638 time to fit residues: 28.5936 Evaluate side-chains 118 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.0980 chunk 84 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.134133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.114206 restraints weight = 14502.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.117486 restraints weight = 8443.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.119642 restraints weight = 5777.255| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6922 Z= 0.246 Angle : 0.604 8.964 9419 Z= 0.301 Chirality : 0.043 0.150 1023 Planarity : 0.004 0.053 1200 Dihedral : 9.121 102.145 988 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.23 % Favored : 95.66 % Rotamer: Outliers : 3.81 % Allowed : 21.47 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.30), residues: 852 helix: 1.93 (0.32), residues: 291 sheet: -0.72 (0.54), residues: 83 loop : 0.15 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 398 HIS 0.005 0.001 HIS D 246 PHE 0.013 0.001 PHE B 118 TYR 0.010 0.001 TYR C 224 ARG 0.004 0.001 ARG C 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 137 THR cc_start: 0.8734 (p) cc_final: 0.8517 (p) REVERT: B 80 ASN cc_start: 0.6882 (t0) cc_final: 0.6503 (t0) REVERT: B 94 ASP cc_start: 0.7563 (t70) cc_final: 0.7308 (t0) REVERT: C 151 LYS cc_start: 0.7929 (mttt) cc_final: 0.7419 (ptpt) outliers start: 27 outliers final: 24 residues processed: 115 average time/residue: 0.1416 time to fit residues: 23.7233 Evaluate side-chains 116 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 389 TYR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 10 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 0.0970 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 4 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.136934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117200 restraints weight = 14385.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.120544 restraints weight = 8346.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.122750 restraints weight = 5664.848| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6922 Z= 0.185 Angle : 0.585 7.813 9419 Z= 0.291 Chirality : 0.042 0.149 1023 Planarity : 0.004 0.052 1200 Dihedral : 8.923 101.400 988 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 3.25 % Allowed : 22.74 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.30), residues: 852 helix: 1.99 (0.32), residues: 291 sheet: -0.83 (0.53), residues: 83 loop : 0.16 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 398 HIS 0.004 0.001 HIS D 246 PHE 0.010 0.001 PHE B 118 TYR 0.010 0.001 TYR B 35 ARG 0.003 0.000 ARG D 163 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 THR cc_start: 0.8792 (p) cc_final: 0.8523 (p) REVERT: B 90 GLU cc_start: 0.8231 (tp30) cc_final: 0.7898 (tp30) REVERT: B 94 ASP cc_start: 0.7494 (t70) cc_final: 0.7159 (m-30) REVERT: C 151 LYS cc_start: 0.7612 (mttt) cc_final: 0.7333 (ptpt) outliers start: 23 outliers final: 21 residues processed: 110 average time/residue: 0.1538 time to fit residues: 24.2418 Evaluate side-chains 111 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 365 CYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 52 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.135381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115432 restraints weight = 14485.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.118737 restraints weight = 8417.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.120995 restraints weight = 5734.458| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6922 Z= 0.216 Angle : 0.611 8.753 9419 Z= 0.300 Chirality : 0.043 0.153 1023 Planarity : 0.004 0.053 1200 Dihedral : 8.927 100.832 987 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.23 % Favored : 95.66 % Rotamer: Outliers : 3.67 % Allowed : 23.31 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.30), residues: 852 helix: 1.97 (0.32), residues: 291 sheet: -0.91 (0.55), residues: 73 loop : 0.13 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 398 HIS 0.004 0.001 HIS D 246 PHE 0.015 0.001 PHE A 36 TYR 0.009 0.001 TYR C 280 ARG 0.005 0.001 ARG C 277 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 THR cc_start: 0.8725 (p) cc_final: 0.8426 (p) outliers start: 26 outliers final: 23 residues processed: 107 average time/residue: 0.1492 time to fit residues: 23.0602 Evaluate side-chains 109 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 365 CYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 55 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 0.0770 chunk 20 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.136780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117347 restraints weight = 14220.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120655 restraints weight = 8007.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.122896 restraints weight = 5344.584| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6922 Z= 0.204 Angle : 0.607 8.121 9419 Z= 0.301 Chirality : 0.042 0.152 1023 Planarity : 0.004 0.052 1200 Dihedral : 8.890 100.903 987 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.11 % Favored : 95.77 % Rotamer: Outliers : 3.53 % Allowed : 23.73 % Favored : 72.74 % 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: 1.02 (0.30), residues: 852 helix: 1.99 (0.32), residues: 291 sheet: -0.83 (0.56), residues: 73 loop : 0.19 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 398 HIS 0.004 0.001 HIS D 246 PHE 0.017 0.001 PHE A 36 TYR 0.029 0.001 TYR C 298 ARG 0.005 0.001 ARG A 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2142.22 seconds wall clock time: 39 minutes 21.11 seconds (2361.11 seconds total)