Starting phenix.real_space_refine on Tue Mar 11 22:47:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fhb_50444/03_2025/9fhb_50444.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fhb_50444/03_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_50444/03_2025/9fhb_50444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fhb_50444/03_2025/9fhb_50444.map" model { file = "/net/cci-nas-00/data/ceres_data/9fhb_50444/03_2025/9fhb_50444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fhb_50444/03_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-5624/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: 4.43, per 1000 atoms: 0.66 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: 1.66 Conformation dependent library (CDL) restraints added in 888.7 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: 0.87 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: 1.95 Time building geometry restraints manager: 1.97 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: 2.610 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.150 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.000 ------------------------------------------------------------------------------- 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 : 0.752 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: 0.1675 time to fit residues: 33.8573 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 : 0.814 ------------------------------------------------------------------------------- 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 = 0.120203 restraints weight = 14167.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.123542 restraints weight = 8031.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.125724 restraints weight = 5398.458| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.696 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: 0.8103 (m-10) cc_final: 0.7420 (m-10) REVERT: C 242 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6791 (m-80) REVERT: C 354 ASP cc_start: 0.7626 (m-30) cc_final: 0.7385 (m-30) REVERT: D 360 ASP cc_start: 0.8458 (m-30) cc_final: 0.7948 (m-30) REVERT: D 396 LYS cc_start: 0.8322 (pttt) cc_final: 0.7887 (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: 0.1645 time to fit residues: 31.7081 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 : 0.753 ------------------------------------------------------------------------------- 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: 3.9990 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 0.0770 chunk 67 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.139842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.119665 restraints weight = 14340.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.122991 restraints weight = 8087.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.125204 restraints weight = 5446.820| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6922 Z= 0.198 Angle : 0.595 7.845 9419 Z= 0.300 Chirality : 0.043 0.150 1023 Planarity : 0.004 0.046 1200 Dihedral : 9.560 108.608 997 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 4.10 % Allowed : 18.08 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.29), residues: 852 helix: 2.27 (0.32), residues: 283 sheet: -0.42 (0.54), residues: 77 loop : 0.01 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 37 HIS 0.002 0.001 HIS A 122 PHE 0.020 0.002 PHE A 36 TYR 0.015 0.001 TYR B 35 ARG 0.009 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 140 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 TYR cc_start: 0.8297 (m-80) cc_final: 0.7720 (m-10) REVERT: C 354 ASP cc_start: 0.7892 (m-30) cc_final: 0.7460 (m-30) REVERT: D 396 LYS cc_start: 0.8322 (pttt) cc_final: 0.7982 (pttt) REVERT: D 436 TRP cc_start: 0.8519 (m-90) cc_final: 0.8309 (m-10) outliers start: 29 outliers final: 17 residues processed: 131 average time/residue: 0.1388 time to fit residues: 26.1971 Evaluate side-chains 117 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 222 THR Chi-restraints excluded: chain C residue 236 VAL 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 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: 0.7980 chunk 53 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114141 restraints weight = 14607.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.117449 restraints weight = 8416.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.119593 restraints weight = 5745.524| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 6922 Z= 0.268 Angle : 0.614 9.005 9419 Z= 0.311 Chirality : 0.044 0.162 1023 Planarity : 0.004 0.045 1200 Dihedral : 9.478 106.832 989 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.17 % Favored : 96.71 % Rotamer: Outliers : 4.66 % Allowed : 19.21 % Favored : 76.13 % 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: 1.05 (0.29), residues: 852 helix: 1.86 (0.32), residues: 292 sheet: -0.05 (0.54), residues: 73 loop : 0.18 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 37 HIS 0.004 0.001 HIS D 246 PHE 0.017 0.002 PHE A 36 TYR 0.013 0.002 TYR B 35 ARG 0.005 0.001 ARG D 179 *********************** 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 143 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 THR cc_start: 0.8791 (p) cc_final: 0.8545 (p) REVERT: B 35 TYR cc_start: 0.8513 (m-80) cc_final: 0.7999 (m-10) REVERT: B 80 ASN cc_start: 0.6926 (t0) cc_final: 0.6581 (t0) REVERT: C 242 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6897 (m-80) REVERT: D 328 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8181 (mm) REVERT: D 396 LYS cc_start: 0.8494 (pttt) cc_final: 0.8244 (pttt) REVERT: D 436 TRP cc_start: 0.8631 (m-10) cc_final: 0.8429 (m-10) outliers start: 33 outliers final: 24 residues processed: 131 average time/residue: 0.1758 time to fit residues: 31.8122 Evaluate side-chains 125 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 B residue 99 ASP Chi-restraints excluded: chain B residue 137 VAL 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 261 ARG 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 157 LEU Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 373 LEU 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: 1.9990 chunk 60 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 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** ** 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 = 0.3800 r_free = 0.3800 target = 0.136049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115788 restraints weight = 14347.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119086 restraints weight = 8297.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121242 restraints weight = 5666.410| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3100 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= 0.214 Angle : 0.590 7.519 9419 Z= 0.298 Chirality : 0.042 0.148 1023 Planarity : 0.004 0.049 1200 Dihedral : 9.279 105.259 989 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.40 % Favored : 96.48 % Rotamer: Outliers : 4.38 % Allowed : 19.07 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.29), residues: 852 helix: 1.89 (0.32), residues: 292 sheet: -0.30 (0.52), residues: 73 loop : 0.18 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 398 HIS 0.005 0.001 HIS A 103 PHE 0.019 0.001 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 141 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 137 THR cc_start: 0.8782 (p) cc_final: 0.8534 (p) REVERT: B 35 TYR cc_start: 0.8442 (m-80) cc_final: 0.7959 (m-10) REVERT: B 80 ASN cc_start: 0.6862 (t0) cc_final: 0.6497 (t0) REVERT: B 90 GLU cc_start: 0.8216 (tp30) cc_final: 0.7326 (tp30) REVERT: B 94 ASP cc_start: 0.7359 (t70) cc_final: 0.7041 (m-30) REVERT: D 328 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8205 (mm) REVERT: D 396 LYS cc_start: 0.8355 (pttt) cc_final: 0.8123 (pttt) outliers start: 31 outliers final: 20 residues processed: 132 average time/residue: 0.1571 time to fit residues: 29.3079 Evaluate side-chains 121 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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 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 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: 0.9990 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.134450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.114222 restraints weight = 14538.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.117504 restraints weight = 8448.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.119691 restraints weight = 5780.605| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6922 Z= 0.237 Angle : 0.591 7.652 9419 Z= 0.297 Chirality : 0.042 0.148 1023 Planarity : 0.004 0.050 1200 Dihedral : 9.222 103.026 989 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.87 % Favored : 96.01 % Rotamer: Outliers : 4.38 % Allowed : 19.77 % Favored : 75.85 % 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: 1.89 (0.32), residues: 292 sheet: -0.70 (0.53), residues: 82 loop : 0.16 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 398 HIS 0.005 0.001 HIS D 246 PHE 0.014 0.002 PHE A 36 TYR 0.010 0.001 TYR C 224 ARG 0.007 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: 31 poor density : 106 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 THR cc_start: 0.8779 (p) cc_final: 0.8515 (p) REVERT: B 35 TYR cc_start: 0.8456 (m-80) cc_final: 0.7965 (m-10) REVERT: B 80 ASN cc_start: 0.6894 (t0) cc_final: 0.6464 (t0) REVERT: B 90 GLU cc_start: 0.8263 (tp30) cc_final: 0.7430 (tp30) REVERT: B 94 ASP cc_start: 0.7450 (t70) cc_final: 0.7013 (m-30) REVERT: C 242 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.6929 (m-80) outliers start: 31 outliers final: 27 residues processed: 122 average time/residue: 0.1548 time to fit residues: 26.6784 Evaluate side-chains 131 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 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 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 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 373 LEU Chi-restraints excluded: chain D residue 471 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 0.0470 chunk 25 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 GLN ** 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 = 0.3791 r_free = 0.3791 target = 0.135474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115427 restraints weight = 14392.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.118753 restraints weight = 8390.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.120918 restraints weight = 5722.665| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6922 Z= 0.200 Angle : 0.572 7.758 9419 Z= 0.287 Chirality : 0.042 0.147 1023 Planarity : 0.004 0.051 1200 Dihedral : 9.077 101.908 989 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 4.10 % Allowed : 20.62 % 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: 0.95 (0.30), residues: 852 helix: 1.95 (0.32), residues: 292 sheet: -0.74 (0.53), residues: 83 loop : 0.14 (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 0.013 0.001 PHE A 36 TYR 0.010 0.001 TYR C 280 ARG 0.006 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 138 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.8431 (t80) cc_final: 0.8152 (t80) REVERT: A 137 THR cc_start: 0.8750 (p) cc_final: 0.8485 (p) REVERT: B 90 GLU cc_start: 0.8220 (tp30) cc_final: 0.7412 (tp30) REVERT: B 94 ASP cc_start: 0.7395 (t70) cc_final: 0.7085 (m-30) outliers start: 29 outliers final: 25 residues processed: 129 average time/residue: 0.1535 time to fit residues: 27.9504 Evaluate side-chains 121 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 187 THR 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 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 365 CYS 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: 1.9990 chunk 72 optimal weight: 4.9990 chunk 32 optimal weight: 0.0980 chunk 27 optimal weight: 0.0270 chunk 84 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 GLN ** 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 = 0.3815 r_free = 0.3815 target = 0.137263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.117429 restraints weight = 14428.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120751 restraints weight = 8346.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.122964 restraints weight = 5658.619| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6922 Z= 0.178 Angle : 0.569 8.357 9419 Z= 0.281 Chirality : 0.041 0.151 1023 Planarity : 0.004 0.050 1200 Dihedral : 8.860 100.101 989 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.52 % Favored : 96.36 % Rotamer: Outliers : 3.67 % Allowed : 22.32 % 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: 0.93 (0.30), residues: 852 helix: 1.92 (0.32), residues: 298 sheet: -0.68 (0.55), residues: 73 loop : 0.06 (0.29), residues: 481 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 0.011 0.001 PHE C 377 TYR 0.010 0.001 TYR B 35 ARG 0.005 0.000 ARG B 40 *********************** 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 128 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 THR cc_start: 0.8815 (p) cc_final: 0.8580 (p) REVERT: B 90 GLU cc_start: 0.8220 (tp30) cc_final: 0.7870 (tp30) REVERT: B 94 ASP cc_start: 0.7454 (t70) cc_final: 0.7089 (m-30) outliers start: 26 outliers final: 24 residues processed: 120 average time/residue: 0.1464 time to fit residues: 25.0618 Evaluate side-chains 117 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 93 CYS Chi-restraints excluded: chain B residue 99 ASP 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.2394 > 50: distance: 44 - 48: 10.905 distance: 48 - 49: 12.326 distance: 49 - 50: 27.576 distance: 49 - 52: 12.401 distance: 50 - 51: 11.595 distance: 50 - 55: 5.350 distance: 51 - 75: 21.902 distance: 52 - 53: 15.839 distance: 52 - 54: 22.323 distance: 55 - 56: 16.408 distance: 55 - 61: 28.518 distance: 56 - 57: 3.896 distance: 56 - 59: 4.184 distance: 57 - 58: 12.586 distance: 57 - 62: 9.471 distance: 58 - 82: 33.905 distance: 59 - 60: 30.095 distance: 60 - 61: 13.536 distance: 62 - 63: 3.084 distance: 63 - 64: 14.973 distance: 63 - 66: 10.626 distance: 64 - 65: 25.158 distance: 64 - 70: 9.649 distance: 65 - 90: 23.009 distance: 66 - 67: 4.656 distance: 67 - 69: 39.367 distance: 70 - 71: 6.760 distance: 71 - 72: 3.180 distance: 71 - 74: 5.306 distance: 72 - 73: 13.175 distance: 72 - 75: 4.768 distance: 73 - 94: 18.368 distance: 75 - 76: 20.812 distance: 76 - 77: 26.096 distance: 76 - 79: 26.591 distance: 77 - 78: 6.005 distance: 77 - 82: 12.894 distance: 79 - 80: 28.131 distance: 79 - 81: 29.696 distance: 82 - 83: 42.536 distance: 83 - 84: 10.193 distance: 83 - 86: 16.890 distance: 84 - 85: 35.744 distance: 84 - 90: 7.011 distance: 86 - 87: 18.618 distance: 87 - 88: 16.791 distance: 88 - 89: 35.237 distance: 90 - 91: 30.292 distance: 91 - 92: 20.170 distance: 92 - 93: 14.186 distance: 92 - 94: 21.669 distance: 94 - 95: 4.509 distance: 95 - 96: 5.933 distance: 95 - 98: 11.088 distance: 96 - 97: 3.009 distance: 96 - 102: 20.406 distance: 97 - 125: 18.560 distance: 98 - 99: 18.373 distance: 99 - 100: 17.084 distance: 99 - 101: 22.510 distance: 102 - 103: 9.229 distance: 102 - 108: 13.533 distance: 103 - 104: 9.646 distance: 103 - 106: 15.153 distance: 104 - 105: 3.951 distance: 104 - 109: 12.807 distance: 105 - 133: 26.431 distance: 106 - 107: 23.475 distance: 107 - 108: 15.208 distance: 109 - 110: 15.592 distance: 110 - 111: 8.884 distance: 110 - 113: 7.462 distance: 111 - 112: 9.438 distance: 111 - 118: 3.205 distance: 112 - 138: 11.327 distance: 113 - 114: 23.400 distance: 114 - 115: 8.940 distance: 115 - 116: 20.612 distance: 116 - 117: 19.131