Starting phenix.real_space_refine on Sat Dec 28 01:53:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uqi_42469/12_2024/8uqi_42469.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uqi_42469/12_2024/8uqi_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_42469/12_2024/8uqi_42469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uqi_42469/12_2024/8uqi_42469.map" model { file = "/net/cci-nas-00/data/ceres_data/8uqi_42469/12_2024/8uqi_42469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uqi_42469/12_2024/8uqi_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-5532/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: 4.75, per 1000 atoms: 0.65 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: 1.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.85 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: 2.08 Time building geometry restraints manager: 2.09 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: 0.00 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.110 Find NCS groups from input model: 0.200 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.690 ------------------------------------------------------------------------------- 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= 0.201 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 *********************** 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 : 0.434 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: 0.1518 time to fit residues: 8.6068 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 : 0.459 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 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= 0.366 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 : 26.10 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 B 463 HIS 0.009 0.001 HIS B 187 PHE 0.016 0.002 PHE B 460 TYR 0.027 0.004 TYR A 201 ARG 0.009 0.001 ARG A 457 *********************** 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 : 0.420 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.8643 (ppp) cc_final: 0.8274 (ppp) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 0.1535 time to fit residues: 10.7166 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 : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 9.9990 chunk 27 optimal weight: 0.0980 chunk 72 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.0470 chunk 94 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 20.0000 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 2.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7482 Z= 0.278 Angle : 0.971 11.405 10196 Z= 0.555 Chirality : 0.047 0.229 1158 Planarity : 0.007 0.063 1342 Dihedral : 8.000 59.857 1058 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 2.09 % Allowed : 5.01 % Favored : 92.90 % Rotamer: Outliers : 0.54 % Allowed : 8.63 % Favored : 90.84 % 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: -1.36 (0.26), residues: 958 helix: 0.33 (0.27), residues: 346 sheet: -1.07 (0.37), residues: 152 loop : -1.82 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 437 HIS 0.009 0.001 HIS B 187 PHE 0.007 0.002 PHE A 155 TYR 0.015 0.002 TYR A 398 ARG 0.006 0.001 ARG A 468 *********************** 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 : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8991 (ppp) cc_final: 0.8386 (ppp) REVERT: A 258 PHE cc_start: 0.9184 (t80) cc_final: 0.8726 (t80) REVERT: A 323 LEU cc_start: 0.8977 (pp) cc_final: 0.8509 (mm) outliers start: 2 outliers final: 0 residues processed: 54 average time/residue: 0.1546 time to fit residues: 10.5915 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 : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 8.9990 chunk 65 optimal weight: 0.0010 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 0.0870 chunk 92 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 overall best weight: 0.9566 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 2.2654 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= 0.245 Angle : 0.900 10.280 10196 Z= 0.522 Chirality : 0.048 0.223 1158 Planarity : 0.006 0.056 1342 Dihedral : 7.501 64.396 1058 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 1.04 % Allowed : 6.68 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % 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: -1.10 (0.26), residues: 958 helix: 0.63 (0.28), residues: 336 sheet: -0.98 (0.36), residues: 152 loop : -1.66 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 72 HIS 0.012 0.001 HIS A 187 PHE 0.006 0.001 PHE A 188 TYR 0.036 0.003 TYR A 201 ARG 0.004 0.000 ARG B 162 *********************** 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 55 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9828 (mp) cc_final: 0.9386 (tp) REVERT: A 117 MET cc_start: 0.8972 (ppp) cc_final: 0.8532 (ppp) REVERT: A 180 MET cc_start: 0.9601 (pmm) cc_final: 0.9337 (pmm) REVERT: A 476 ARG cc_start: 0.9799 (ppt170) cc_final: 0.9533 (ttp80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1755 time to fit residues: 11.9931 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 : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 38 optimal weight: 0.0970 chunk 79 optimal weight: 0.0070 chunk 64 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 83 optimal weight: 0.6980 chunk 23 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 overall best weight: 0.3174 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 2.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7482 Z= 0.234 Angle : 0.888 11.103 10196 Z= 0.507 Chirality : 0.046 0.179 1158 Planarity : 0.006 0.053 1342 Dihedral : 7.094 62.431 1058 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 1.25 % Allowed : 4.80 % Favored : 93.95 % 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: -0.78 (0.27), residues: 958 helix: 0.83 (0.28), residues: 336 sheet: -0.57 (0.38), residues: 162 loop : -1.54 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 437 HIS 0.005 0.001 HIS B 168 PHE 0.008 0.001 PHE B 155 TYR 0.025 0.003 TYR B 398 ARG 0.008 0.000 ARG B 162 *********************** 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 : 0.390 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.9051 (ppp) cc_final: 0.8484 (ppp) REVERT: A 180 MET cc_start: 0.9556 (pmm) cc_final: 0.9225 (pmm) REVERT: A 186 MET cc_start: 0.7388 (tpp) cc_final: 0.7159 (tpp) REVERT: A 476 ARG cc_start: 0.9806 (ppt170) cc_final: 0.9529 (ttp80) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1564 time to fit residues: 10.3609 Evaluate side-chains 33 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.0980 chunk 18 optimal weight: 0.0470 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 0.0470 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 2.3090 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= 0.226 Angle : 0.873 11.273 10196 Z= 0.498 Chirality : 0.046 0.170 1158 Planarity : 0.006 0.050 1342 Dihedral : 6.747 63.254 1058 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 1.04 % Allowed : 5.64 % Favored : 93.32 % Rotamer: Outliers : 0.27 % Allowed : 5.39 % Favored : 94.34 % 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: -0.64 (0.27), residues: 958 helix: 0.86 (0.28), residues: 338 sheet: -0.13 (0.40), residues: 146 loop : -1.50 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 426 HIS 0.007 0.001 HIS A 187 PHE 0.006 0.001 PHE A 427 TYR 0.026 0.003 TYR B 398 ARG 0.007 0.000 ARG A 162 *********************** 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 53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 117 MET cc_start: 0.9035 (ppp) cc_final: 0.8544 (ppp) REVERT: A 180 MET cc_start: 0.9561 (pmm) cc_final: 0.9205 (pmm) REVERT: A 201 TYR cc_start: 0.8572 (m-80) cc_final: 0.8340 (m-80) REVERT: A 460 PHE cc_start: 0.4763 (OUTLIER) cc_final: 0.4183 (m-80) REVERT: A 464 GLU cc_start: 0.9340 (tm-30) cc_final: 0.9123 (tm-30) REVERT: A 476 ARG cc_start: 0.9796 (ppt170) cc_final: 0.9529 (ttp80) outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.1246 time to fit residues: 8.7593 Evaluate side-chains 38 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 92 optimal weight: 0.0570 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 0.0770 chunk 42 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 2.3242 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= 0.223 Angle : 0.882 11.067 10196 Z= 0.500 Chirality : 0.046 0.183 1158 Planarity : 0.006 0.053 1342 Dihedral : 6.697 64.644 1058 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 1.04 % Allowed : 5.43 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: -0.50 (0.27), residues: 958 helix: 0.97 (0.28), residues: 338 sheet: 0.07 (0.41), residues: 136 loop : -1.43 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 426 HIS 0.008 0.001 HIS A 187 PHE 0.015 0.002 PHE B 460 TYR 0.025 0.002 TYR B 398 ARG 0.006 0.000 ARG A 162 *********************** 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 54 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8921 (ppp) cc_final: 0.8425 (ppp) REVERT: A 476 ARG cc_start: 0.9801 (ppt170) cc_final: 0.9534 (ttp80) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1466 time to fit residues: 10.1569 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 : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 0.0270 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 0.0020 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 overall best weight: 0.3846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 2.3328 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= 0.221 Angle : 0.879 11.743 10196 Z= 0.495 Chirality : 0.046 0.196 1158 Planarity : 0.006 0.061 1342 Dihedral : 6.564 64.637 1058 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 1.04 % Allowed : 5.43 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: -0.44 (0.27), residues: 958 helix: 0.98 (0.28), residues: 338 sheet: 0.08 (0.41), residues: 136 loop : -1.36 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 426 HIS 0.009 0.001 HIS A 187 PHE 0.015 0.002 PHE B 485 TYR 0.027 0.002 TYR B 398 ARG 0.006 0.000 ARG B 203 *********************** 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 49 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.9100 (ppp) cc_final: 0.8695 (ppp) REVERT: A 180 MET cc_start: 0.9407 (pmm) cc_final: 0.9193 (pmm) REVERT: A 476 ARG cc_start: 0.9796 (ppt170) cc_final: 0.9515 (ttp80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1512 time to fit residues: 9.6918 Evaluate side-chains 36 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.4980 chunk 88 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 37 optimal weight: 0.0170 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 0.0470 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 2.3471 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= 0.222 Angle : 0.881 11.639 10196 Z= 0.498 Chirality : 0.046 0.204 1158 Planarity : 0.006 0.052 1342 Dihedral : 6.528 64.968 1058 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 1.04 % Allowed : 5.64 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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: -0.37 (0.27), residues: 958 helix: 1.05 (0.28), residues: 334 sheet: -0.35 (0.38), residues: 164 loop : -1.16 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 426 HIS 0.011 0.001 HIS A 187 PHE 0.012 0.002 PHE A 155 TYR 0.030 0.003 TYR B 201 ARG 0.006 0.000 ARG B 203 *********************** 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 : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.9204 (ppp) cc_final: 0.8825 (ppp) REVERT: A 180 MET cc_start: 0.9353 (pmm) cc_final: 0.9132 (pmm) REVERT: A 476 ARG cc_start: 0.9792 (ppt170) cc_final: 0.9494 (ttp80) REVERT: A 485 PHE cc_start: 0.8960 (m-80) cc_final: 0.8700 (m-80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1249 time to fit residues: 8.2474 Evaluate side-chains 36 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 63 optimal weight: 0.0370 chunk 95 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 81 optimal weight: 0.0040 overall best weight: 0.5470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 2.3524 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= 0.218 Angle : 0.873 12.341 10196 Z= 0.492 Chirality : 0.046 0.220 1158 Planarity : 0.007 0.069 1342 Dihedral : 6.454 65.234 1058 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.84 % Allowed : 5.64 % Favored : 93.53 % 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: 1.08 (0.28), residues: 334 sheet: -0.22 (0.42), residues: 152 loop : -1.22 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 426 HIS 0.009 0.001 HIS A 187 PHE 0.010 0.002 PHE A 155 TYR 0.028 0.002 TYR A 398 ARG 0.007 0.000 ARG B 203 ********************** 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 51 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LEU cc_start: 0.9823 (mm) cc_final: 0.9406 (tp) REVERT: A 117 MET cc_start: 0.9202 (ppp) cc_final: 0.8811 (ppp) REVERT: A 180 MET cc_start: 0.9364 (pmm) cc_final: 0.9145 (pmm) REVERT: A 476 ARG cc_start: 0.9788 (ppt170) cc_final: 0.9567 (ttp80) REVERT: A 485 PHE cc_start: 0.8972 (m-80) cc_final: 0.8725 (m-80) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1422 time to fit residues: 9.4240 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 : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 40.0000 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 9 optimal weight: 0.0470 chunk 14 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.065044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.052042 restraints weight = 39520.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.053350 restraints weight = 23813.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.054151 restraints weight = 16353.240| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 2.3674 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= 0.226 Angle : 0.877 12.146 10196 Z= 0.497 Chirality : 0.047 0.238 1158 Planarity : 0.006 0.054 1342 Dihedral : 6.471 65.505 1058 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 1.04 % Allowed : 5.43 % Favored : 93.53 % 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: -0.41 (0.27), residues: 958 helix: 1.00 (0.28), residues: 334 sheet: -0.35 (0.42), residues: 152 loop : -1.17 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 426 HIS 0.009 0.001 HIS A 187 PHE 0.013 0.002 PHE A 460 TYR 0.031 0.003 TYR B 201 ARG 0.008 0.000 ARG B 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1490.08 seconds wall clock time: 28 minutes 25.16 seconds (1705.16 seconds total)