Starting phenix.real_space_refine on Sat Dec 28 02:11:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uqk_42472/12_2024/8uqk_42472.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uqk_42472/12_2024/8uqk_42472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uqk_42472/12_2024/8uqk_42472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uqk_42472/12_2024/8uqk_42472.map" model { file = "/net/cci-nas-00/data/ceres_data/8uqk_42472/12_2024/8uqk_42472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uqk_42472/12_2024/8uqk_42472.cif" } resolution = 4.61 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 13 residue(s): 0.02s 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: "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} 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} Time building chain proxies: 4.98, per 1000 atoms: 0.68 Number of scatterers: 7318 At special positions: 0 Unit cell: (78.07, 114.995, 121.325, 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: 1.92 Conformation dependent library (CDL) restraints added in 903.4 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: 41 helices and 6 sheets defined 42.5% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'B' and resid 17 through 21 Processing helix chain 'B' and resid 44 through 52 removed outlier: 3.717A pdb=" N GLN B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU B 50 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 3.774A 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 removed outlier: 3.658A pdb=" N VAL B 66 " --> pdb=" O THR B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 73 Processing helix chain 'B' and resid 74 through 82 removed outlier: 4.813A pdb=" N ALA B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 removed outlier: 4.016A pdb=" N ARG B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 154 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 319 removed outlier: 3.560A pdb=" N CYS B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL B 292 " --> pdb=" O ARG B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 327 Processing helix chain 'B' and resid 332 through 340 Processing helix chain 'B' and resid 340 through 349 removed outlier: 3.549A pdb=" N VAL B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR B 348 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 381 removed outlier: 4.111A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 399 through 402 Processing helix chain 'B' and resid 460 through 468 Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.513A pdb=" N LEU B 479 " --> pdb=" O LYS B 475 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 487 removed outlier: 3.508A pdb=" N PHE B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 21 Processing helix chain 'A' and resid 44 through 52 removed outlier: 3.712A pdb=" N GLN A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU A 50 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.509A pdb=" N TRP A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 82 removed outlier: 4.475A pdb=" N ALA A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 removed outlier: 3.578A pdb=" N SER A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 154 removed outlier: 3.828A pdb=" N LEU A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 151 " --> pdb=" O ASN A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.506A pdb=" N ASP A 192 " --> pdb=" O PRO A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 242 through 253 Processing helix chain 'A' and resid 283 through 319 removed outlier: 3.540A pdb=" N ARG A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 327 removed outlier: 3.897A pdb=" N SER A 326 " --> pdb=" O PRO A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 340 removed outlier: 3.831A pdb=" N ASP A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 removed outlier: 3.633A pdb=" N VAL A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR A 348 " --> pdb=" O VAL A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 380 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 399 through 405 Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.840A pdb=" N LEU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 487 removed outlier: 3.770A pdb=" N PHE A 485 " --> pdb=" O ALA A 481 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 33 removed outlier: 3.563A pdb=" N THR B 104 " --> pdb=" O PHE B 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 187 through 188 removed outlier: 3.813A pdb=" N LEU B 172 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL B 160 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLU B 174 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL B 158 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 271 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS B 264 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 388 through 390 removed outlier: 3.736A pdb=" N PHE B 389 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 29 through 33 removed outlier: 3.974A pdb=" N VAL A 29 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU A 108 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 33 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 104 " --> pdb=" O PHE A 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 188 removed outlier: 3.809A pdb=" N LEU A 172 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL A 160 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLU A 174 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL A 158 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A 262 " --> pdb=" O TRP A 269 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU A 271 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 260 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA A 273 " --> pdb=" O PHE A 258 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE A 258 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS A 275 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA A 256 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A 207 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 355 removed outlier: 3.510A pdb=" N GLY A 352 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A 354 " --> pdb=" O LEU A 425 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 783 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: 2.00 Time building geometry restraints manager: 2.20 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: 2519 1.34 - 1.46: 1454 1.46 - 1.58: 3479 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 7482 Sorted by residual: bond pdb=" N PRO A 54 " pdb=" CA PRO A 54 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.31e-02 5.83e+03 1.79e+00 bond pdb=" N VAL A 254 " pdb=" CA VAL A 254 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.19e-02 7.06e+03 1.22e+00 bond pdb=" CA ASP A 116 " pdb=" CB ASP A 116 " ideal model delta sigma weight residual 1.527 1.545 -0.018 1.70e-02 3.46e+03 1.14e+00 bond pdb=" N VAL B 254 " pdb=" CA VAL B 254 " ideal model delta sigma weight residual 1.460 1.474 -0.014 1.42e-02 4.96e+03 9.76e-01 bond pdb=" C VAL B 224 " pdb=" O VAL B 224 " ideal model delta sigma weight residual 1.232 1.241 -0.008 8.90e-03 1.26e+04 8.61e-01 ... (remaining 7477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 9975 2.45 - 4.89: 197 4.89 - 7.34: 21 7.34 - 9.78: 1 9.78 - 12.23: 2 Bond angle restraints: 10196 Sorted by residual: angle pdb=" N GLY B 358 " pdb=" CA GLY B 358 " pdb=" C GLY B 358 " ideal model delta sigma weight residual 114.25 109.51 4.74 1.30e+00 5.92e-01 1.33e+01 angle pdb=" C PRO A 115 " pdb=" N ASP A 116 " pdb=" CA ASP A 116 " ideal model delta sigma weight residual 122.46 127.59 -5.13 1.41e+00 5.03e-01 1.33e+01 angle pdb=" CA LEU A 122 " pdb=" CB LEU A 122 " pdb=" CG LEU A 122 " ideal model delta sigma weight residual 116.30 128.53 -12.23 3.50e+00 8.16e-02 1.22e+01 angle pdb=" N GLU A 123 " pdb=" CA GLU A 123 " pdb=" C GLU A 123 " ideal model delta sigma weight residual 112.23 107.92 4.31 1.26e+00 6.30e-01 1.17e+01 angle pdb=" N ALA A 83 " pdb=" CA ALA A 83 " pdb=" C ALA A 83 " ideal model delta sigma weight residual 108.46 113.37 -4.91 1.51e+00 4.39e-01 1.06e+01 ... (remaining 10191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4115 17.62 - 35.24: 364 35.24 - 52.86: 44 52.86 - 70.48: 11 70.48 - 88.10: 8 Dihedral angle restraints: 4542 sinusoidal: 1792 harmonic: 2750 Sorted by residual: dihedral pdb=" CA SER A 388 " pdb=" C SER A 388 " pdb=" N PHE A 389 " pdb=" CA PHE A 389 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ASP A 156 " pdb=" C ASP A 156 " pdb=" N ARG A 157 " pdb=" CA ARG A 157 " ideal model delta harmonic sigma weight residual -180.00 -159.17 -20.83 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ALA A 83 " pdb=" C ALA A 83 " pdb=" N LEU A 84 " pdb=" CA LEU A 84 " ideal model delta harmonic sigma weight residual 180.00 159.32 20.68 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 4539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 842 0.038 - 0.076: 220 0.076 - 0.113: 77 0.113 - 0.151: 16 0.151 - 0.189: 3 Chirality restraints: 1158 Sorted by residual: chirality pdb=" CG LEU B 206 " pdb=" CB LEU B 206 " pdb=" CD1 LEU B 206 " pdb=" CD2 LEU B 206 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA ASP A 116 " pdb=" N ASP A 116 " pdb=" C ASP A 116 " pdb=" CB ASP A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA ARG B 457 " pdb=" N ARG B 457 " pdb=" C ARG B 457 " pdb=" CB ARG B 457 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 1155 not shown) Planarity restraints: 1342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 229 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.26e+00 pdb=" N PRO A 230 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 88 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO B 89 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 89 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 89 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 88 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO A 89 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " 0.026 5.00e-02 4.00e+02 ... (remaining 1339 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 463 2.73 - 3.27: 8434 3.27 - 3.81: 13029 3.81 - 4.36: 15043 4.36 - 4.90: 23143 Nonbonded interactions: 60112 Sorted by model distance: nonbonded pdb=" O VAL B 149 " pdb=" OG1 THR B 153 " model vdw 2.184 3.040 nonbonded pdb=" O PRO A 322 " pdb=" OG1 THR A 325 " model vdw 2.204 3.040 nonbonded pdb=" OE2 GLU A 312 " pdb=" NZ LYS A 475 " model vdw 2.212 3.120 nonbonded pdb=" O PRO B 456 " pdb=" N GLY B 458 " model vdw 2.224 3.120 nonbonded pdb=" O SER A 44 " pdb=" OG1 THR A 47 " model vdw 2.234 3.040 ... (remaining 60107 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.110 Find NCS groups from input model: 0.210 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 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 0.036 7482 Z= 0.198 Angle : 0.862 12.226 10196 Z= 0.486 Chirality : 0.040 0.189 1158 Planarity : 0.006 0.063 1342 Dihedral : 13.606 88.100 2766 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.47 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -2.07 (0.25), residues: 958 helix: -0.56 (0.27), residues: 304 sheet: -1.72 (0.40), residues: 142 loop : -1.77 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 379 HIS 0.006 0.001 HIS B 455 PHE 0.011 0.001 PHE A 385 TYR 0.012 0.002 TYR B 93 ARG 0.006 0.001 ARG B 404 *********************** 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 38 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.419 Fit side-chains REVERT: A 75 TRP cc_start: 0.9520 (t60) cc_final: 0.9203 (t60) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.2420 time to fit residues: 10.9900 Evaluate side-chains 20 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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: 0.3980 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 0.0970 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 38 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 0.0570 chunk 87 optimal weight: 0.8980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** 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: 0.6934 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7482 Z= 0.222 Angle : 0.802 11.596 10196 Z= 0.390 Chirality : 0.045 0.177 1158 Planarity : 0.006 0.071 1342 Dihedral : 5.669 21.375 1058 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.64 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % 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: -1.95 (0.25), residues: 958 helix: -0.40 (0.28), residues: 312 sheet: -0.80 (0.41), residues: 142 loop : -2.06 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.003 0.001 HIS A 455 PHE 0.007 0.001 PHE B 258 TYR 0.012 0.002 TYR A 284 ARG 0.031 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.426 Fit side-chains REVERT: A 268 LEU cc_start: 0.9065 (tp) cc_final: 0.8224 (tp) REVERT: A 360 GLU cc_start: 0.9224 (pm20) cc_final: 0.8872 (pp20) REVERT: A 401 LEU cc_start: 0.9762 (tp) cc_final: 0.9561 (tp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1490 time to fit residues: 8.1889 Evaluate side-chains 23 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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: 10.0000 chunk 27 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 94 optimal weight: 0.0670 chunk 77 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 40.0000 overall best weight: 1.2920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** 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: 0.6970 moved from start: 0.6643 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 : 0.751 12.048 10196 Z= 0.363 Chirality : 0.042 0.149 1158 Planarity : 0.006 0.051 1342 Dihedral : 5.404 23.186 1058 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.14 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: -2.56 (0.24), residues: 958 helix: -1.23 (0.26), residues: 332 sheet: -1.08 (0.39), residues: 160 loop : -2.27 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 379 HIS 0.003 0.001 HIS A 315 PHE 0.005 0.001 PHE A 389 TYR 0.006 0.001 TYR B 398 ARG 0.014 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.420 Fit side-chains REVERT: A 159 MET cc_start: 0.8711 (tpp) cc_final: 0.8384 (tpp) REVERT: A 360 GLU cc_start: 0.9306 (pm20) cc_final: 0.8983 (pp20) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1179 time to fit residues: 6.2705 Evaluate side-chains 22 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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: 10.0000 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 0.0000 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** 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: 0.6996 moved from start: 0.6859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7482 Z= 0.184 Angle : 0.723 11.559 10196 Z= 0.347 Chirality : 0.042 0.165 1158 Planarity : 0.005 0.038 1342 Dihedral : 5.299 22.328 1058 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.14 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % 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: -2.53 (0.24), residues: 958 helix: -1.25 (0.26), residues: 328 sheet: -0.81 (0.40), residues: 150 loop : -2.29 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 75 HIS 0.003 0.001 HIS B 451 PHE 0.012 0.002 PHE A 389 TYR 0.011 0.001 TYR B 248 ARG 0.011 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.445 Fit side-chains REVERT: A 171 VAL cc_start: 0.7703 (t) cc_final: 0.7479 (t) REVERT: A 258 PHE cc_start: 0.8399 (t80) cc_final: 0.7381 (t80) REVERT: A 260 LEU cc_start: 0.9001 (mm) cc_final: 0.8338 (mm) REVERT: A 360 GLU cc_start: 0.9316 (pm20) cc_final: 0.8898 (pp20) REVERT: A 362 LEU cc_start: 0.9538 (tt) cc_final: 0.9159 (mp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1175 time to fit residues: 6.5456 Evaluate side-chains 26 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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: 6.9990 chunk 1 optimal weight: 0.0570 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.0570 chunk 83 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.3820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** 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: 0.6982 moved from start: 0.7198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7482 Z= 0.176 Angle : 0.719 10.737 10196 Z= 0.341 Chirality : 0.042 0.154 1158 Planarity : 0.005 0.039 1342 Dihedral : 4.924 21.629 1058 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.52 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % 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: -2.61 (0.24), residues: 958 helix: -1.49 (0.25), residues: 344 sheet: -0.57 (0.41), residues: 150 loop : -2.32 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 75 HIS 0.004 0.001 HIS B 451 PHE 0.011 0.001 PHE B 258 TYR 0.009 0.001 TYR A 161 ARG 0.010 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.368 Fit side-chains REVERT: A 171 VAL cc_start: 0.7497 (t) cc_final: 0.7208 (t) REVERT: A 258 PHE cc_start: 0.8447 (t80) cc_final: 0.7491 (t80) REVERT: A 360 GLU cc_start: 0.9289 (pm20) cc_final: 0.8897 (pp20) REVERT: A 362 LEU cc_start: 0.9381 (tt) cc_final: 0.9169 (mp) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1535 time to fit residues: 7.4659 Evaluate side-chains 26 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.0770 chunk 92 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 0.5980 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** 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: 0.7044 moved from start: 0.7278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7482 Z= 0.187 Angle : 0.725 10.591 10196 Z= 0.347 Chirality : 0.041 0.154 1158 Planarity : 0.005 0.037 1342 Dihedral : 5.071 20.929 1058 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.77 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: -2.60 (0.24), residues: 958 helix: -1.52 (0.25), residues: 332 sheet: -0.72 (0.40), residues: 150 loop : -2.21 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 437 HIS 0.004 0.001 HIS B 451 PHE 0.019 0.002 PHE A 385 TYR 0.012 0.001 TYR B 248 ARG 0.008 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.583 Fit side-chains REVERT: A 258 PHE cc_start: 0.8436 (t80) cc_final: 0.7547 (t80) REVERT: A 360 GLU cc_start: 0.9383 (pm20) cc_final: 0.9141 (mm-30) REVERT: A 370 MET cc_start: 0.9774 (tpt) cc_final: 0.9566 (tpt) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1542 time to fit residues: 7.5857 Evaluate side-chains 27 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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: 0.8980 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 0.0370 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 0.0870 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 0.0870 chunk 42 optimal weight: 0.0570 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 0.0040 overall best weight: 0.0544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** 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: 0.7007 moved from start: 0.7493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7482 Z= 0.185 Angle : 0.734 9.463 10196 Z= 0.347 Chirality : 0.042 0.177 1158 Planarity : 0.005 0.048 1342 Dihedral : 4.915 22.517 1058 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.14 % Favored : 91.65 % 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 : 0.00 % 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: -2.63 (0.24), residues: 958 helix: -1.60 (0.25), residues: 346 sheet: -0.60 (0.39), residues: 150 loop : -2.24 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 75 HIS 0.005 0.001 HIS B 451 PHE 0.014 0.001 PHE A 258 TYR 0.008 0.001 TYR A 398 ARG 0.009 0.001 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.462 Fit side-chains REVERT: A 258 PHE cc_start: 0.8506 (t80) cc_final: 0.7669 (t80) REVERT: A 360 GLU cc_start: 0.9299 (pm20) cc_final: 0.9044 (mm-30) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1477 time to fit residues: 7.6593 Evaluate side-chains 26 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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: 4.9990 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 0.0000 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** 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: 0.7043 moved from start: 0.7515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7482 Z= 0.180 Angle : 0.716 9.805 10196 Z= 0.345 Chirality : 0.041 0.171 1158 Planarity : 0.006 0.059 1342 Dihedral : 4.894 21.547 1058 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.56 % Favored : 91.23 % 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 : 0.00 % 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: -2.63 (0.24), residues: 958 helix: -1.58 (0.25), residues: 344 sheet: -0.68 (0.39), residues: 150 loop : -2.21 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 426 HIS 0.004 0.001 HIS B 451 PHE 0.012 0.001 PHE A 258 TYR 0.010 0.001 TYR B 248 ARG 0.011 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.402 Fit side-chains REVERT: A 258 PHE cc_start: 0.8447 (t80) cc_final: 0.7494 (t80) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1483 time to fit residues: 6.9125 Evaluate side-chains 21 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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: 0.7980 chunk 37 optimal weight: 0.0030 chunk 67 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 0.0270 chunk 85 optimal weight: 0.0030 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.1256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** 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: 0.7018 moved from start: 0.7735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7482 Z= 0.177 Angle : 0.727 9.278 10196 Z= 0.346 Chirality : 0.042 0.160 1158 Planarity : 0.005 0.044 1342 Dihedral : 4.791 21.275 1058 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.35 % Favored : 91.44 % 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 : 0.00 % 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: -2.52 (0.24), residues: 958 helix: -1.56 (0.25), residues: 344 sheet: -0.54 (0.39), residues: 150 loop : -2.12 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 426 HIS 0.005 0.001 HIS B 451 PHE 0.016 0.002 PHE B 389 TYR 0.008 0.001 TYR B 161 ARG 0.010 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.488 Fit side-chains revert: symmetry clash REVERT: A 258 PHE cc_start: 0.8405 (t80) cc_final: 0.7496 (t80) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1560 time to fit residues: 7.1353 Evaluate side-chains 28 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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: 0.0040 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 chunk 95 optimal weight: 0.0980 chunk 88 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 7 optimal weight: 0.0040 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 81 optimal weight: 0.5980 overall best weight: 0.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** 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: 0.7028 moved from start: 0.7940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7482 Z= 0.194 Angle : 0.755 8.584 10196 Z= 0.360 Chirality : 0.042 0.152 1158 Planarity : 0.005 0.042 1342 Dihedral : 4.771 20.907 1058 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.93 % Favored : 91.86 % 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 : 0.00 % 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: -2.69 (0.24), residues: 958 helix: -1.83 (0.23), residues: 346 sheet: -0.44 (0.41), residues: 140 loop : -2.14 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 167 HIS 0.005 0.001 HIS B 451 PHE 0.012 0.001 PHE A 258 TYR 0.016 0.002 TYR B 161 ARG 0.003 0.000 ARG A 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.419 Fit side-chains revert: symmetry clash REVERT: A 258 PHE cc_start: 0.8400 (t80) cc_final: 0.7597 (t80) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1487 time to fit residues: 7.1499 Evaluate side-chains 24 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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: 0.6980 chunk 70 optimal weight: 0.4980 chunk 11 optimal weight: 0.0670 chunk 21 optimal weight: 0.0050 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.3932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** 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 = 0.3504 r_free = 0.3504 target = 0.058761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.046156 restraints weight = 35950.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.047375 restraints weight = 26120.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.048319 restraints weight = 20531.220| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.8026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7482 Z= 0.183 Angle : 0.729 8.685 10196 Z= 0.348 Chirality : 0.042 0.158 1158 Planarity : 0.005 0.040 1342 Dihedral : 4.696 19.856 1058 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.93 % Favored : 91.86 % 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 : 0.00 % 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: -2.62 (0.24), residues: 958 helix: -1.70 (0.24), residues: 346 sheet: -1.08 (0.37), residues: 176 loop : -1.95 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 426 HIS 0.005 0.001 HIS B 451 PHE 0.010 0.001 PHE A 389 TYR 0.007 0.001 TYR B 248 ARG 0.012 0.001 ARG A 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1483.49 seconds wall clock time: 27 minutes 55.55 seconds (1675.55 seconds total)