Starting phenix.real_space_refine on Fri Jul 25 08:56:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uqi_42469/07_2025/8uqi_42469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uqi_42469/07_2025/8uqi_42469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uqi_42469/07_2025/8uqi_42469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uqi_42469/07_2025/8uqi_42469.map" model { file = "/net/cci-nas-00/data/ceres_data/8uqi_42469/07_2025/8uqi_42469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uqi_42469/07_2025/8uqi_42469.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 4630 2.51 5 N 1332 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7318 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3659 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 445} Chain: "B" Number of atoms: 3659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3659 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 445} Time building chain proxies: 4.99, per 1000 atoms: 0.68 Number of scatterers: 7318 At special positions: 0 Unit cell: (72.584, 109.72, 114.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 1338 8.00 N 1332 7.00 C 4630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 977.5 milliseconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 42.6% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 11 through 16 removed outlier: 3.867A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.577A pdb=" N VAL A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 67' Processing helix chain 'A' and resid 68 through 82 removed outlier: 4.364A pdb=" N GLU A 76 " --> pdb=" O TRP A 72 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 removed outlier: 4.050A pdb=" N THR A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 154 removed outlier: 3.618A pdb=" N LEU A 141 " --> pdb=" O GLY A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 194 through 204 removed outlier: 3.694A pdb=" N ARG A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 252 removed outlier: 4.267A pdb=" N MET A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 330 removed outlier: 4.095A pdb=" N VAL A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 3.834A pdb=" N GLY A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 340 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 398 through 404 removed outlier: 3.709A pdb=" N ALA A 402 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A 404 " --> pdb=" O PRO A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 Processing helix chain 'A' and resid 448 through 452 removed outlier: 4.419A pdb=" N ALA A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 45 through 52 removed outlier: 3.994A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 50 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 59 Processing helix chain 'B' and resid 62 through 67 Processing helix chain 'B' and resid 68 through 73 Processing helix chain 'B' and resid 74 through 82 removed outlier: 4.782A pdb=" N ALA B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.934A pdb=" N ARG B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 removed outlier: 3.853A pdb=" N LEU B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 242 through 253 Processing helix chain 'B' and resid 283 through 327 removed outlier: 3.511A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL B 292 " --> pdb=" O ARG B 288 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Proline residue: B 322 - end of helix Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.782A pdb=" N ASP B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 349 removed outlier: 4.095A pdb=" N GLU B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU B 347 " --> pdb=" O ARG B 343 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR B 348 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 381 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.631A pdb=" N GLY B 439 " --> pdb=" O SER B 436 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN B 440 " --> pdb=" O TRP B 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 436 through 440' Processing helix chain 'B' and resid 460 through 468 Processing helix chain 'B' and resid 475 through 487 removed outlier: 3.972A pdb=" N LEU B 479 " --> pdb=" O LYS B 475 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 87 removed outlier: 3.546A pdb=" N HIS A 98 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 87 removed outlier: 4.124A pdb=" N THR A 104 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 33 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU A 30 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL A 43 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA A 32 " --> pdb=" O GLU A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 176 removed outlier: 3.974A pdb=" N CYS A 274 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE A 258 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG A 207 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 187 Processing sheet with id=AA5, first strand: chain 'A' and resid 353 through 356 removed outlier: 3.588A pdb=" N ALA A 354 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 100 Processing sheet with id=AA9, first strand: chain 'B' and resid 170 through 174 removed outlier: 5.931A pdb=" N VAL B 171 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG B 162 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 262 " --> pdb=" O TRP B 269 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU B 271 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 260 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA B 273 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE B 258 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N HIS B 275 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ALA B 256 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG B 207 " --> pdb=" O SER B 259 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 352 through 355 removed outlier: 3.559A pdb=" N GLY B 352 " --> pdb=" O PHE B 427 " (cutoff:3.500A) 303 hydrogen bonds defined for protein. 831 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: 2.21 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2514 1.34 - 1.46: 1343 1.46 - 1.58: 3595 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 7482 Sorted by residual: bond pdb=" CA PRO B 384 " pdb=" C PRO B 384 " ideal model delta sigma weight residual 1.526 1.518 0.008 8.50e-03 1.38e+04 9.70e-01 bond pdb=" CA ASP B 116 " pdb=" CB ASP B 116 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.70e-02 3.46e+03 9.59e-01 bond pdb=" C LYS A 136 " pdb=" N GLY A 137 " ideal model delta sigma weight residual 1.319 1.332 -0.013 1.44e-02 4.82e+03 8.48e-01 bond pdb=" C THR A 351 " pdb=" O THR A 351 " ideal model delta sigma weight residual 1.235 1.245 -0.010 1.10e-02 8.26e+03 8.08e-01 bond pdb=" N PRO A 399 " pdb=" CA PRO A 399 " ideal model delta sigma weight residual 1.465 1.483 -0.018 2.03e-02 2.43e+03 7.89e-01 ... (remaining 7477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 9837 2.05 - 4.09: 319 4.09 - 6.14: 29 6.14 - 8.19: 9 8.19 - 10.23: 2 Bond angle restraints: 10196 Sorted by residual: angle pdb=" N GLY A 137 " pdb=" CA GLY A 137 " pdb=" C GLY A 137 " ideal model delta sigma weight residual 110.20 115.83 -5.63 1.32e+00 5.74e-01 1.82e+01 angle pdb=" N GLU B 123 " pdb=" CA GLU B 123 " pdb=" C GLU B 123 " ideal model delta sigma weight residual 112.89 108.39 4.50 1.24e+00 6.50e-01 1.32e+01 angle pdb=" N ALA B 83 " pdb=" CA ALA B 83 " pdb=" C ALA B 83 " ideal model delta sigma weight residual 108.46 113.62 -5.16 1.51e+00 4.39e-01 1.17e+01 angle pdb=" N VAL B 432 " pdb=" CA VAL B 432 " pdb=" C VAL B 432 " ideal model delta sigma weight residual 111.62 108.95 2.67 7.90e-01 1.60e+00 1.14e+01 angle pdb=" C SER A 283 " pdb=" N TYR A 284 " pdb=" CA TYR A 284 " ideal model delta sigma weight residual 120.44 124.74 -4.30 1.30e+00 5.92e-01 1.09e+01 ... (remaining 10191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4101 17.84 - 35.67: 380 35.67 - 53.51: 45 53.51 - 71.35: 12 71.35 - 89.18: 4 Dihedral angle restraints: 4542 sinusoidal: 1792 harmonic: 2750 Sorted by residual: dihedral pdb=" CA ASP B 156 " pdb=" C ASP B 156 " pdb=" N ARG B 157 " pdb=" CA ARG B 157 " ideal model delta harmonic sigma weight residual -180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LYS B 176 " pdb=" C LYS B 176 " pdb=" N ARG B 177 " pdb=" CA ARG B 177 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ALA B 83 " pdb=" C ALA B 83 " pdb=" N LEU B 84 " pdb=" CA LEU B 84 " ideal model delta harmonic sigma weight residual 180.00 159.56 20.44 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 4539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 880 0.044 - 0.088: 217 0.088 - 0.132: 56 0.132 - 0.176: 4 0.176 - 0.220: 1 Chirality restraints: 1158 Sorted by residual: chirality pdb=" CB VAL A 373 " pdb=" CA VAL A 373 " pdb=" CG1 VAL A 373 " pdb=" CG2 VAL A 373 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ASP B 116 " pdb=" N ASP B 116 " pdb=" C ASP B 116 " pdb=" CB ASP B 116 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CB VAL A 160 " pdb=" CA VAL A 160 " pdb=" CG1 VAL A 160 " pdb=" CG2 VAL A 160 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 1155 not shown) Planarity restraints: 1342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 229 " 0.033 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO B 230 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 230 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 230 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 399 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO A 400 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 400 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 400 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 204 " -0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 205 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " -0.027 5.00e-02 4.00e+02 ... (remaining 1339 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 252 2.67 - 3.23: 7983 3.23 - 3.79: 12850 3.79 - 4.34: 16390 4.34 - 4.90: 24082 Nonbonded interactions: 61557 Sorted by model distance: nonbonded pdb=" OG1 THR A 332 " pdb=" OE1 GLU A 335 " model vdw 2.118 3.040 nonbonded pdb=" O ASN A 204 " pdb=" NH1 ARG A 207 " model vdw 2.154 3.120 nonbonded pdb=" O GLN A 300 " pdb=" OG SER A 303 " model vdw 2.163 3.040 nonbonded pdb=" O ALA A 199 " pdb=" OG1 THR A 202 " model vdw 2.171 3.040 nonbonded pdb=" OG SER B 369 " pdb=" OD1 ASP B 371 " model vdw 2.172 3.040 ... (remaining 61552 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.230 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.270 Find NCS groups from input model: 0.250 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7482 Z= 0.157 Angle : 0.836 10.233 10196 Z= 0.469 Chirality : 0.041 0.220 1158 Planarity : 0.006 0.051 1342 Dihedral : 13.618 89.182 2766 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.13 % Allowed : 0.67 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.83 (0.26), residues: 958 helix: 0.02 (0.30), residues: 301 sheet: -2.52 (0.41), residues: 121 loop : -1.64 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 72 HIS 0.003 0.001 HIS B 455 PHE 0.009 0.001 PHE A 155 TYR 0.021 0.002 TYR A 398 ARG 0.004 0.000 ARG B 81 Details of bonding type rmsd hydrogen bonds : bond 0.19684 ( 297) hydrogen bonds : angle 8.53993 ( 831) covalent geometry : bond 0.00294 ( 7482) covalent geometry : angle 0.83574 (10196) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.449 Fit side-chains REVERT: A 31 LEU cc_start: 0.9709 (mp) cc_final: 0.9457 (mp) REVERT: A 117 MET cc_start: 0.8760 (ppp) cc_final: 0.8353 (ppp) REVERT: A 485 PHE cc_start: 0.9111 (m-10) cc_final: 0.8874 (m-80) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1530 time to fit residues: 8.7668 Evaluate side-chains 30 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 0.0050 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 0.0010 chunk 87 optimal weight: 0.0980 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.058233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.045811 restraints weight = 40848.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.047077 restraints weight = 23002.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.047916 restraints weight = 15299.810| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 2.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 7482 Z= 0.317 Angle : 1.120 13.216 10196 Z= 0.643 Chirality : 0.057 0.480 1158 Planarity : 0.010 0.129 1342 Dihedral : 8.688 63.691 1058 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 26.03 Ramachandran Plot: Outliers : 5.01 % Allowed : 7.31 % Favored : 87.68 % Rotamer: Outliers : 1.62 % Allowed : 10.78 % Favored : 87.60 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.26), residues: 958 helix: 0.15 (0.27), residues: 330 sheet: -1.37 (0.39), residues: 136 loop : -2.07 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 463 HIS 0.009 0.001 HIS A 187 PHE 0.016 0.002 PHE A 460 TYR 0.027 0.004 TYR A 201 ARG 0.009 0.001 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.22008 ( 297) hydrogen bonds : angle 8.59274 ( 831) covalent geometry : bond 0.00550 ( 7482) covalent geometry : angle 1.12016 (10196) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.8502 (ppp) cc_final: 0.8099 (ppp) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.1493 time to fit residues: 10.2999 Evaluate side-chains 40 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.0570 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.060171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.047809 restraints weight = 40419.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.049091 restraints weight = 22821.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.049973 restraints weight = 15111.102| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 2.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7482 Z= 0.240 Angle : 0.975 11.230 10196 Z= 0.556 Chirality : 0.048 0.244 1158 Planarity : 0.007 0.062 1342 Dihedral : 8.002 60.073 1058 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 1.88 % Allowed : 5.22 % Favored : 92.90 % Rotamer: Outliers : 0.54 % Allowed : 8.36 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.12 % 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: -1.38 (0.26), residues: 958 helix: 0.26 (0.27), residues: 346 sheet: -1.03 (0.38), residues: 152 loop : -1.81 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 437 HIS 0.008 0.001 HIS A 187 PHE 0.016 0.002 PHE A 155 TYR 0.013 0.002 TYR A 398 ARG 0.005 0.001 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.18263 ( 297) hydrogen bonds : angle 8.25049 ( 831) covalent geometry : bond 0.00421 ( 7482) covalent geometry : angle 0.97492 (10196) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8841 (ppp) cc_final: 0.8218 (ppp) REVERT: A 258 PHE cc_start: 0.9073 (t80) cc_final: 0.8830 (t80) REVERT: A 323 LEU cc_start: 0.8911 (pp) cc_final: 0.8489 (mm) outliers start: 2 outliers final: 0 residues processed: 54 average time/residue: 0.1479 time to fit residues: 10.2240 Evaluate side-chains 35 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 24 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 51 optimal weight: 0.0770 chunk 71 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 33 optimal weight: 0.0970 overall best weight: 1.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.059269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.046715 restraints weight = 41183.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.048008 restraints weight = 23138.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.048854 restraints weight = 15400.149| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 2.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7482 Z= 0.219 Angle : 0.892 10.233 10196 Z= 0.518 Chirality : 0.048 0.234 1158 Planarity : 0.007 0.059 1342 Dihedral : 7.551 64.158 1058 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 1.04 % Allowed : 6.68 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.90 % 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: -1.11 (0.26), residues: 958 helix: 0.64 (0.28), residues: 336 sheet: -1.11 (0.36), residues: 152 loop : -1.65 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 379 HIS 0.013 0.001 HIS A 187 PHE 0.012 0.002 PHE A 460 TYR 0.033 0.003 TYR B 201 ARG 0.004 0.000 ARG B 162 Details of bonding type rmsd hydrogen bonds : bond 0.16657 ( 297) hydrogen bonds : angle 8.11766 ( 831) covalent geometry : bond 0.00369 ( 7482) covalent geometry : angle 0.89229 (10196) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9698 (mp) cc_final: 0.9346 (tp) REVERT: A 117 MET cc_start: 0.8826 (ppp) cc_final: 0.8356 (ppp) REVERT: A 180 MET cc_start: 0.9544 (pmm) cc_final: 0.9289 (pmm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1635 time to fit residues: 11.0411 Evaluate side-chains 37 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 43 optimal weight: 0.0060 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 0.0020 chunk 39 optimal weight: 0.0970 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 70 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 79 optimal weight: 0.0070 overall best weight: 0.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.062817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.049877 restraints weight = 40807.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.051202 restraints weight = 23182.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.052079 restraints weight = 15414.616| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 2.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7482 Z= 0.214 Angle : 0.897 11.250 10196 Z= 0.511 Chirality : 0.046 0.172 1158 Planarity : 0.006 0.054 1342 Dihedral : 7.171 62.547 1058 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 1.04 % Allowed : 5.22 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.90 % 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: -0.79 (0.26), residues: 958 helix: 0.88 (0.28), residues: 332 sheet: -0.38 (0.39), residues: 146 loop : -1.62 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 437 HIS 0.004 0.001 HIS B 168 PHE 0.010 0.001 PHE B 155 TYR 0.024 0.003 TYR B 398 ARG 0.008 0.001 ARG B 162 Details of bonding type rmsd hydrogen bonds : bond 0.16291 ( 297) hydrogen bonds : angle 7.91643 ( 831) covalent geometry : bond 0.00364 ( 7482) covalent geometry : angle 0.89686 (10196) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.8953 (ppp) cc_final: 0.8368 (ppp) REVERT: A 180 MET cc_start: 0.9475 (pmm) cc_final: 0.9151 (pmm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1313 time to fit residues: 9.0248 Evaluate side-chains 32 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 46 optimal weight: 10.0000 chunk 21 optimal weight: 0.0470 chunk 73 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 36 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 20 optimal weight: 0.0370 chunk 87 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.062992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.049818 restraints weight = 40899.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.051134 restraints weight = 23408.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.051933 restraints weight = 15694.990| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 2.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7482 Z= 0.202 Angle : 0.874 11.479 10196 Z= 0.497 Chirality : 0.045 0.170 1158 Planarity : 0.006 0.051 1342 Dihedral : 6.832 63.250 1058 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 1.04 % Allowed : 5.43 % Favored : 93.53 % Rotamer: Outliers : 0.27 % Allowed : 3.77 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.67 % 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: -0.65 (0.27), residues: 958 helix: 0.88 (0.28), residues: 334 sheet: -0.18 (0.40), residues: 146 loop : -1.50 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 426 HIS 0.007 0.001 HIS A 187 PHE 0.005 0.001 PHE A 155 TYR 0.025 0.002 TYR A 398 ARG 0.008 0.000 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.15798 ( 297) hydrogen bonds : angle 7.88479 ( 831) covalent geometry : bond 0.00334 ( 7482) covalent geometry : angle 0.87393 (10196) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.9034 (ppp) cc_final: 0.8356 (ppp) REVERT: A 163 PHE cc_start: 0.9552 (m-10) cc_final: 0.9340 (m-10) REVERT: A 180 MET cc_start: 0.8494 (pmm) cc_final: 0.8067 (pmm) REVERT: A 201 TYR cc_start: 0.8413 (m-80) cc_final: 0.8184 (m-80) REVERT: A 258 PHE cc_start: 0.9241 (t80) cc_final: 0.8989 (t80) REVERT: A 370 MET cc_start: 0.9799 (pmm) cc_final: 0.9582 (pmm) REVERT: A 460 PHE cc_start: 0.3568 (OUTLIER) cc_final: 0.3055 (m-80) REVERT: A 464 GLU cc_start: 0.9342 (tm-30) cc_final: 0.9079 (tm-30) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.1266 time to fit residues: 8.5330 Evaluate side-chains 36 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 0.0970 chunk 17 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.0010 chunk 86 optimal weight: 0.3980 chunk 76 optimal weight: 0.2980 chunk 77 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.063661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.050622 restraints weight = 40319.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.051898 restraints weight = 23154.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.052801 restraints weight = 15667.274| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 2.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7482 Z= 0.201 Angle : 0.880 10.969 10196 Z= 0.500 Chirality : 0.045 0.174 1158 Planarity : 0.006 0.050 1342 Dihedral : 6.703 64.568 1058 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 1.04 % Allowed : 5.43 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -0.52 (0.27), residues: 958 helix: 1.05 (0.28), residues: 334 sheet: -0.35 (0.38), residues: 152 loop : -1.39 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 426 HIS 0.008 0.001 HIS A 187 PHE 0.018 0.002 PHE B 460 TYR 0.025 0.002 TYR B 398 ARG 0.006 0.000 ARG A 162 Details of bonding type rmsd hydrogen bonds : bond 0.15544 ( 297) hydrogen bonds : angle 7.79575 ( 831) covalent geometry : bond 0.00336 ( 7482) covalent geometry : angle 0.87978 (10196) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8936 (ppp) cc_final: 0.8373 (ppp) REVERT: A 180 MET cc_start: 0.9550 (pmm) cc_final: 0.9212 (pmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1329 time to fit residues: 8.8716 Evaluate side-chains 35 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 51 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 0.2980 chunk 91 optimal weight: 0.0070 chunk 67 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 8.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.064135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.051180 restraints weight = 40408.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.052420 restraints weight = 23234.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.053347 restraints weight = 15763.213| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 2.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7482 Z= 0.196 Angle : 0.881 11.747 10196 Z= 0.495 Chirality : 0.046 0.189 1158 Planarity : 0.006 0.050 1342 Dihedral : 6.565 64.446 1058 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 1.04 % Allowed : 5.22 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -0.42 (0.27), residues: 958 helix: 1.05 (0.28), residues: 334 sheet: -0.05 (0.41), residues: 136 loop : -1.32 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 426 HIS 0.008 0.001 HIS A 187 PHE 0.015 0.002 PHE A 485 TYR 0.027 0.002 TYR B 398 ARG 0.008 0.000 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.15491 ( 297) hydrogen bonds : angle 7.82018 ( 831) covalent geometry : bond 0.00324 ( 7482) covalent geometry : angle 0.88072 (10196) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8933 (ppp) cc_final: 0.8512 (ppp) REVERT: A 180 MET cc_start: 0.9557 (pmm) cc_final: 0.9216 (pmm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1731 time to fit residues: 10.8320 Evaluate side-chains 35 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 53 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 41 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 63 optimal weight: 0.0070 chunk 66 optimal weight: 0.5980 chunk 88 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.064026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.051135 restraints weight = 40117.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.052414 restraints weight = 23362.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.053316 restraints weight = 15818.061| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 2.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7482 Z= 0.197 Angle : 0.881 11.494 10196 Z= 0.498 Chirality : 0.046 0.185 1158 Planarity : 0.006 0.052 1342 Dihedral : 6.555 64.863 1058 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 1.04 % Allowed : 5.64 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -0.36 (0.27), residues: 958 helix: 1.10 (0.28), residues: 334 sheet: -0.01 (0.41), residues: 136 loop : -1.28 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 426 HIS 0.008 0.001 HIS A 187 PHE 0.013 0.002 PHE A 155 TYR 0.027 0.002 TYR B 398 ARG 0.007 0.000 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.15396 ( 297) hydrogen bonds : angle 7.74693 ( 831) covalent geometry : bond 0.00332 ( 7482) covalent geometry : angle 0.88102 (10196) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8958 (ppp) cc_final: 0.8551 (ppp) REVERT: A 180 MET cc_start: 0.9488 (pmm) cc_final: 0.9119 (pmm) REVERT: A 485 PHE cc_start: 0.8863 (m-80) cc_final: 0.8599 (m-80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1193 time to fit residues: 7.7986 Evaluate side-chains 38 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 30.0000 chunk 61 optimal weight: 0.0970 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 54 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.063809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.051034 restraints weight = 40209.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.052295 restraints weight = 23219.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.053190 restraints weight = 15811.093| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 2.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7482 Z= 0.195 Angle : 0.870 12.225 10196 Z= 0.492 Chirality : 0.045 0.180 1158 Planarity : 0.006 0.054 1342 Dihedral : 6.470 65.123 1058 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.84 % Allowed : 5.85 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -0.34 (0.27), residues: 958 helix: 1.14 (0.29), residues: 334 sheet: -0.12 (0.43), residues: 136 loop : -1.25 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 426 HIS 0.010 0.001 HIS A 187 PHE 0.012 0.002 PHE A 155 TYR 0.036 0.004 TYR B 201 ARG 0.006 0.000 ARG B 207 Details of bonding type rmsd hydrogen bonds : bond 0.15379 ( 297) hydrogen bonds : angle 7.72091 ( 831) covalent geometry : bond 0.00329 ( 7482) covalent geometry : angle 0.87039 (10196) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8998 (ppp) cc_final: 0.8579 (ppp) REVERT: A 180 MET cc_start: 0.9504 (pmm) cc_final: 0.9139 (pmm) REVERT: A 485 PHE cc_start: 0.8868 (m-80) cc_final: 0.8612 (m-80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1629 time to fit residues: 10.6481 Evaluate side-chains 39 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 91 optimal weight: 0.4980 chunk 58 optimal weight: 0.4980 chunk 66 optimal weight: 0.4980 chunk 15 optimal weight: 0.0870 chunk 56 optimal weight: 0.0170 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 46 optimal weight: 0.0060 chunk 90 optimal weight: 0.0970 overall best weight: 0.1410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.066079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.053150 restraints weight = 39272.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.054460 restraints weight = 23038.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.055391 restraints weight = 15618.848| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 2.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7482 Z= 0.198 Angle : 0.882 12.454 10196 Z= 0.495 Chirality : 0.045 0.195 1158 Planarity : 0.006 0.053 1342 Dihedral : 6.438 65.324 1058 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 1.04 % Allowed : 5.43 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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 (0.27), residues: 958 helix: 0.98 (0.28), residues: 334 sheet: -0.07 (0.43), residues: 136 loop : -1.23 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 426 HIS 0.011 0.001 HIS A 187 PHE 0.011 0.002 PHE A 460 TYR 0.028 0.003 TYR B 398 ARG 0.005 0.000 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.15448 ( 297) hydrogen bonds : angle 7.64392 ( 831) covalent geometry : bond 0.00331 ( 7482) covalent geometry : angle 0.88191 (10196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2054.47 seconds wall clock time: 37 minutes 10.00 seconds (2230.00 seconds total)