Starting phenix.real_space_refine on Thu Jul 2 05:50:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xn4_33310/07_2026/7xn4_33310.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xn4_33310/07_2026/7xn4_33310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xn4_33310/07_2026/7xn4_33310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xn4_33310/07_2026/7xn4_33310.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xn4_33310/07_2026/7xn4_33310.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xn4_33310/07_2026/7xn4_33310.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xn4_33310/07_2026/7xn4_33310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xn4_33310/07_2026/7xn4_33310.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 1.000 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 38 5.16 5 C 4335 2.51 5 N 1209 2.21 5 O 1275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6859 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1706 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 2 Chain: "B" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3256 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain: "C" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1387 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain breaks: 5 Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.62, per 1000 atoms: 0.24 Number of scatterers: 6859 At special positions: 0 Unit cell: (110.302, 95.988, 74.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 2 15.00 O 1275 8.00 N 1209 7.00 C 4335 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: 0.60 Conformation dependent library (CDL) restraints added in 373.0 milliseconds 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 43.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 67 through 82 removed outlier: 3.598A pdb=" N ALA A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 removed outlier: 3.528A pdb=" N ILE A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 142 removed outlier: 3.576A pdb=" N THR A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 227 removed outlier: 4.298A pdb=" N GLN A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 removed outlier: 3.962A pdb=" N ARG A 238 " --> pdb=" O HIS A 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 74 removed outlier: 4.025A pdb=" N ILE B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 93 through 114 removed outlier: 3.729A pdb=" N LEU B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 129 removed outlier: 4.414A pdb=" N ARG B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.925A pdb=" N GLU B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 removed outlier: 3.635A pdb=" N ARG B 222 " --> pdb=" O PRO B 219 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 Processing helix chain 'B' and resid 256 through 261 removed outlier: 4.538A pdb=" N ARG B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TRP B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 261' Processing helix chain 'B' and resid 278 through 293 removed outlier: 3.894A pdb=" N VAL B 283 " --> pdb=" O MET B 279 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.680A pdb=" N TYR B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 removed outlier: 3.521A pdb=" N SER B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 365 through 378 removed outlier: 3.533A pdb=" N ASP B 378 " --> pdb=" O TRP B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 392 removed outlier: 3.524A pdb=" N GLY B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN B 391 " --> pdb=" O HIS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 401 removed outlier: 3.865A pdb=" N ALA B 400 " --> pdb=" O GLY B 397 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER B 401 " --> pdb=" O ASP B 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 397 through 401' Processing helix chain 'B' and resid 409 through 415 removed outlier: 3.620A pdb=" N SER B 415 " --> pdb=" O ASN B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 429 removed outlier: 3.561A pdb=" N LEU B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 455 removed outlier: 3.677A pdb=" N ASN B 451 " --> pdb=" O THR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 468 removed outlier: 3.648A pdb=" N ALA B 463 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 81 removed outlier: 3.703A pdb=" N LEU C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 102 removed outlier: 4.354A pdb=" N MET C 100 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 removed outlier: 3.568A pdb=" N GLU C 106 " --> pdb=" O VAL C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 107 through 111 removed outlier: 4.095A pdb=" N LYS C 110 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 141 removed outlier: 3.509A pdb=" N ASN C 141 " --> pdb=" O LYS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 213 through 227 removed outlier: 3.663A pdb=" N ALA C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 246 removed outlier: 3.520A pdb=" N ALA C 244 " --> pdb=" O ASN C 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.747A pdb=" N ASN D 111 " --> pdb=" O HIS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 127 removed outlier: 4.066A pdb=" N GLU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 removed outlier: 4.040A pdb=" N GLU D 140 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE D 141 " --> pdb=" O TYR D 138 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL D 142 " --> pdb=" O GLU D 139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89 removed outlier: 5.983A pdb=" N LEU A 46 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL A 117 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE A 48 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU A 119 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE A 50 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS A 116 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLN A 161 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 118 " --> pdb=" O GLN A 161 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER C 267 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 197 " --> pdb=" O CYS C 264 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AA3, first strand: chain 'B' and resid 225 through 226 Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 88 removed outlier: 6.739A pdb=" N CYS C 47 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LYS C 88 " --> pdb=" O CYS C 47 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE C 49 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU C 46 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL C 117 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE C 48 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU C 119 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE C 50 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLN C 161 " --> pdb=" O CYS C 116 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU C 118 " --> pdb=" O GLN C 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 218 hydrogen bonds defined for protein. 615 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: 0.73 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1144 1.29 - 1.42: 1886 1.42 - 1.55: 3903 1.55 - 1.68: 5 1.68 - 1.81: 64 Bond restraints: 7002 Sorted by residual: bond pdb=" CA ASN B 355 " pdb=" C ASN B 355 " ideal model delta sigma weight residual 1.526 1.438 0.087 1.08e-02 8.57e+03 6.53e+01 bond pdb=" CA LYS B 454 " pdb=" C LYS B 454 " ideal model delta sigma weight residual 1.524 1.443 0.081 1.26e-02 6.30e+03 4.09e+01 bond pdb=" C ASN B 443 " pdb=" O ASN B 443 " ideal model delta sigma weight residual 1.235 1.162 0.073 1.26e-02 6.30e+03 3.37e+01 bond pdb=" C VAL B 442 " pdb=" N ASN B 443 " ideal model delta sigma weight residual 1.332 1.253 0.079 1.40e-02 5.10e+03 3.21e+01 bond pdb=" N GLU A 272 " pdb=" CA GLU A 272 " ideal model delta sigma weight residual 1.454 1.389 0.065 1.16e-02 7.43e+03 3.14e+01 ... (remaining 6997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 9342 3.38 - 6.76: 73 6.76 - 10.14: 10 10.14 - 13.52: 4 13.52 - 16.90: 1 Bond angle restraints: 9430 Sorted by residual: angle pdb=" N GLU D 123 " pdb=" CA GLU D 123 " pdb=" C GLU D 123 " ideal model delta sigma weight residual 112.23 104.22 8.01 1.26e+00 6.30e-01 4.04e+01 angle pdb=" O VAL B 442 " pdb=" C VAL B 442 " pdb=" N ASN B 443 " ideal model delta sigma weight residual 123.03 117.08 5.95 1.05e+00 9.07e-01 3.21e+01 angle pdb=" C ASN B 355 " pdb=" CA ASN B 355 " pdb=" CB ASN B 355 " ideal model delta sigma weight residual 111.23 103.22 8.01 1.42e+00 4.96e-01 3.18e+01 angle pdb=" O1A NAD B1001 " pdb=" PA NAD B1001 " pdb=" O2A NAD B1001 " ideal model delta sigma weight residual 122.64 105.74 16.90 3.00e+00 1.11e-01 3.17e+01 angle pdb=" N LEU A 230 " pdb=" CA LEU A 230 " pdb=" C LEU A 230 " ideal model delta sigma weight residual 111.81 119.28 -7.47 1.54e+00 4.22e-01 2.35e+01 ... (remaining 9425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 3639 16.17 - 32.34: 393 32.34 - 48.50: 111 48.50 - 64.67: 15 64.67 - 80.84: 5 Dihedral angle restraints: 4163 sinusoidal: 1681 harmonic: 2482 Sorted by residual: dihedral pdb=" C ASN B 355 " pdb=" N ASN B 355 " pdb=" CA ASN B 355 " pdb=" CB ASN B 355 " ideal model delta harmonic sigma weight residual -122.60 -108.59 -14.01 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" CA PRO B 329 " pdb=" C PRO B 329 " pdb=" N ARG B 330 " pdb=" CA ARG B 330 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLN B 253 " pdb=" C GLN B 253 " pdb=" N MET B 254 " pdb=" CA MET B 254 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 4160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 896 0.065 - 0.131: 99 0.131 - 0.196: 10 0.196 - 0.261: 2 0.261 - 0.326: 2 Chirality restraints: 1009 Sorted by residual: chirality pdb=" CA ASN B 443 " pdb=" N ASN B 443 " pdb=" C ASN B 443 " pdb=" CB ASN B 443 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" C2B NAD B1001 " pdb=" C1B NAD B1001 " pdb=" C3B NAD B1001 " pdb=" O2B NAD B1001 " both_signs ideal model delta sigma weight residual False -2.53 -2.84 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA GLN B 66 " pdb=" N GLN B 66 " pdb=" C GLN B 66 " pdb=" CB GLN B 66 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1006 not shown) Planarity restraints: 1218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 442 " 0.025 2.00e-02 2.50e+03 4.77e-02 2.28e+01 pdb=" C VAL B 442 " -0.083 2.00e-02 2.50e+03 pdb=" O VAL B 442 " 0.029 2.00e-02 2.50e+03 pdb=" N ASN B 443 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 126 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ARG D 126 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG D 126 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU D 127 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 122 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.77e+00 pdb=" C ASP D 122 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP D 122 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU D 123 " 0.017 2.00e-02 2.50e+03 ... (remaining 1215 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1142 2.76 - 3.29: 6485 3.29 - 3.83: 10573 3.83 - 4.36: 13299 4.36 - 4.90: 22625 Nonbonded interactions: 54124 Sorted by model distance: nonbonded pdb=" NE2 GLN B 253 " pdb=" O LYS B 295 " model vdw 2.223 3.120 nonbonded pdb=" O2B NAD B1001 " pdb=" O3B NAD B1001 " model vdw 2.261 2.432 nonbonded pdb=" O GLY B 171 " pdb=" N LEU B 175 " model vdw 2.275 3.120 nonbonded pdb=" OD1 ASN D 97 " pdb=" N GLY D 98 " model vdw 2.279 3.120 nonbonded pdb=" OG SER B 429 " pdb=" ND1 HIS B 467 " model vdw 2.296 3.120 ... (remaining 54119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.380 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.220 Find NCS groups from input model: 0.030 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 7002 Z= 0.318 Angle : 0.795 16.897 9430 Z= 0.404 Chirality : 0.047 0.326 1009 Planarity : 0.005 0.068 1218 Dihedral : 14.679 80.840 2561 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 0.70 % Allowed : 0.70 % Favored : 98.60 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.28), residues: 837 helix: -1.71 (0.26), residues: 305 sheet: -2.94 (0.48), residues: 115 loop : -1.72 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 79 TYR 0.022 0.001 TYR A 37 PHE 0.020 0.001 PHE B 233 TRP 0.013 0.001 TRP C 214 HIS 0.005 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.32 ( 7002) covalent geometry : angle 0.79483 / 0.40 ( 9430) hydrogen bonds : bond 0.25600 / 16.23 ( 218) hydrogen bonds : angle 8.27879 / 5.71 ( 615) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 0.280 Fit side-chains REVERT: A 102 ASP cc_start: 0.7355 (m-30) cc_final: 0.7034 (m-30) REVERT: A 135 ASP cc_start: 0.6982 (p0) cc_final: 0.6332 (t70) REVERT: C 107 ASP cc_start: 0.7442 (t70) cc_final: 0.7105 (t0) REVERT: D 85 ILE cc_start: 0.8045 (pt) cc_final: 0.7838 (mt) REVERT: D 130 ILE cc_start: 0.5948 (mm) cc_final: 0.5373 (tp) outliers start: 5 outliers final: 0 residues processed: 152 average time/residue: 0.0865 time to fit residues: 17.3959 Evaluate side-chains 125 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0170 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS B 244 HIS C 161 GLN D 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.142282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.115580 restraints weight = 11601.656| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.59 r_work: 0.3441 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7002 Z= 0.126 Angle : 0.611 14.426 9430 Z= 0.314 Chirality : 0.042 0.173 1009 Planarity : 0.005 0.049 1218 Dihedral : 5.298 43.359 938 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.84 % Allowed : 8.11 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.28), residues: 837 helix: -1.04 (0.27), residues: 313 sheet: -2.75 (0.44), residues: 129 loop : -1.65 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 79 TYR 0.016 0.001 TYR A 37 PHE 0.012 0.001 PHE A 247 TRP 0.011 0.001 TRP A 214 HIS 0.017 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7002) covalent geometry : angle 0.61079 / 0.31 ( 9430) hydrogen bonds : bond 0.04049 / 2.61 ( 218) hydrogen bonds : angle 5.05218 / 3.49 ( 615) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.260 Fit side-chains REVERT: A 102 ASP cc_start: 0.7726 (m-30) cc_final: 0.7309 (m-30) REVERT: A 135 ASP cc_start: 0.7219 (p0) cc_final: 0.6586 (t70) REVERT: B 302 TYR cc_start: 0.6575 (OUTLIER) cc_final: 0.5836 (t80) REVERT: B 448 MET cc_start: 0.8146 (mtt) cc_final: 0.7856 (mtt) REVERT: C 76 GLU cc_start: 0.7738 (tp30) cc_final: 0.7536 (tp30) REVERT: C 240 ASN cc_start: 0.8463 (t0) cc_final: 0.8249 (t0) outliers start: 6 outliers final: 1 residues processed: 139 average time/residue: 0.0851 time to fit residues: 15.9319 Evaluate side-chains 126 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 302 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 11 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 overall best weight: 1.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.136946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.109502 restraints weight = 11401.443| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.64 r_work: 0.3330 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7002 Z= 0.218 Angle : 0.634 8.853 9430 Z= 0.331 Chirality : 0.044 0.164 1009 Planarity : 0.005 0.053 1218 Dihedral : 5.575 46.834 938 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 1.40 % Allowed : 12.03 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.60 (0.28), residues: 837 helix: -0.98 (0.27), residues: 317 sheet: -2.84 (0.44), residues: 127 loop : -1.87 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 111 TYR 0.012 0.001 TYR B 225 PHE 0.017 0.001 PHE B 78 TRP 0.009 0.001 TRP A 214 HIS 0.007 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 ( 7002) covalent geometry : angle 0.63365 / 0.33 ( 9430) hydrogen bonds : bond 0.04287 / 2.77 ( 218) hydrogen bonds : angle 4.84560 / 3.34 ( 615) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.267 Fit side-chains REVERT: A 102 ASP cc_start: 0.7735 (m-30) cc_final: 0.7307 (m-30) REVERT: A 135 ASP cc_start: 0.7349 (p0) cc_final: 0.6718 (t70) REVERT: A 225 GLN cc_start: 0.8248 (pm20) cc_final: 0.7924 (pm20) REVERT: B 302 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.5866 (t80) outliers start: 10 outliers final: 5 residues processed: 127 average time/residue: 0.0732 time to fit residues: 12.5973 Evaluate side-chains 125 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 377 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 64 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.140308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.114009 restraints weight = 11396.636| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.55 r_work: 0.3420 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7002 Z= 0.135 Angle : 0.586 15.881 9430 Z= 0.299 Chirality : 0.042 0.160 1009 Planarity : 0.004 0.051 1218 Dihedral : 5.343 46.611 938 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 1.54 % Allowed : 13.71 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.28), residues: 837 helix: -0.85 (0.28), residues: 326 sheet: -2.67 (0.44), residues: 127 loop : -1.88 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 79 TYR 0.010 0.001 TYR B 225 PHE 0.012 0.001 PHE B 299 TRP 0.004 0.001 TRP B 261 HIS 0.004 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 7002) covalent geometry : angle 0.58567 / 0.30 ( 9430) hydrogen bonds : bond 0.03383 / 2.19 ( 218) hydrogen bonds : angle 4.49499 / 3.07 ( 615) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.274 Fit side-chains REVERT: A 102 ASP cc_start: 0.7737 (m-30) cc_final: 0.7325 (m-30) REVERT: A 135 ASP cc_start: 0.7301 (p0) cc_final: 0.6762 (t70) REVERT: A 225 GLN cc_start: 0.8245 (pm20) cc_final: 0.7946 (pm20) REVERT: B 302 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.5709 (t80) outliers start: 11 outliers final: 9 residues processed: 137 average time/residue: 0.0768 time to fit residues: 14.4410 Evaluate side-chains 133 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 449 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 0.0000 chunk 83 optimal weight: 7.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.137922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.110149 restraints weight = 11438.141| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.67 r_work: 0.3337 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7002 Z= 0.168 Angle : 0.604 13.411 9430 Z= 0.310 Chirality : 0.043 0.161 1009 Planarity : 0.004 0.052 1218 Dihedral : 5.415 47.015 938 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.68 % Allowed : 16.08 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.28), residues: 837 helix: -0.82 (0.28), residues: 326 sheet: -2.69 (0.44), residues: 127 loop : -1.96 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 79 TYR 0.010 0.001 TYR B 225 PHE 0.013 0.001 PHE B 78 TRP 0.004 0.001 TRP B 261 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 7002) covalent geometry : angle 0.60354 / 0.31 ( 9430) hydrogen bonds : bond 0.03536 / 2.30 ( 218) hydrogen bonds : angle 4.45776 / 3.04 ( 615) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.266 Fit side-chains REVERT: A 102 ASP cc_start: 0.7756 (m-30) cc_final: 0.7336 (m-30) REVERT: A 135 ASP cc_start: 0.7392 (p0) cc_final: 0.6848 (t70) REVERT: A 225 GLN cc_start: 0.8253 (pm20) cc_final: 0.7998 (pm20) REVERT: B 302 TYR cc_start: 0.6667 (OUTLIER) cc_final: 0.5752 (t80) REVERT: B 448 MET cc_start: 0.8286 (mtt) cc_final: 0.8046 (mtt) outliers start: 12 outliers final: 9 residues processed: 131 average time/residue: 0.0738 time to fit residues: 13.4314 Evaluate side-chains 132 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 449 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.140739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.113053 restraints weight = 11345.742| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.65 r_work: 0.3374 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7002 Z= 0.121 Angle : 0.576 14.868 9430 Z= 0.292 Chirality : 0.041 0.158 1009 Planarity : 0.004 0.052 1218 Dihedral : 5.234 46.539 938 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 1.68 % Allowed : 16.64 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.29), residues: 837 helix: -0.66 (0.29), residues: 327 sheet: -2.62 (0.44), residues: 127 loop : -1.88 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.009 0.001 TYR B 225 PHE 0.011 0.001 PHE B 78 TRP 0.006 0.001 TRP A 214 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 7002) covalent geometry : angle 0.57555 / 0.29 ( 9430) hydrogen bonds : bond 0.03052 / 1.94 ( 218) hydrogen bonds : angle 4.33280 / 2.97 ( 615) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.312 Fit side-chains REVERT: A 102 ASP cc_start: 0.7749 (m-30) cc_final: 0.7336 (m-30) REVERT: A 135 ASP cc_start: 0.7261 (p0) cc_final: 0.6780 (t70) REVERT: A 225 GLN cc_start: 0.8226 (pm20) cc_final: 0.7996 (pm20) REVERT: B 302 TYR cc_start: 0.6506 (OUTLIER) cc_final: 0.5591 (t80) REVERT: C 70 ASP cc_start: 0.8537 (p0) cc_final: 0.8021 (p0) REVERT: C 157 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8992 (mt) REVERT: D 97 ASN cc_start: 0.8094 (t0) cc_final: 0.7854 (t0) outliers start: 12 outliers final: 9 residues processed: 127 average time/residue: 0.0777 time to fit residues: 13.7020 Evaluate side-chains 131 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 157 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.137452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.109148 restraints weight = 11528.899| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.67 r_work: 0.3323 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7002 Z= 0.199 Angle : 0.634 14.701 9430 Z= 0.325 Chirality : 0.044 0.164 1009 Planarity : 0.004 0.054 1218 Dihedral : 5.507 47.545 938 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 1.96 % Allowed : 17.20 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.28), residues: 837 helix: -0.79 (0.28), residues: 326 sheet: -2.73 (0.43), residues: 127 loop : -1.96 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 260 TYR 0.011 0.001 TYR B 225 PHE 0.018 0.001 PHE A 128 TRP 0.004 0.001 TRP B 261 HIS 0.006 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 ( 7002) covalent geometry : angle 0.63365 / 0.32 ( 9430) hydrogen bonds : bond 0.03663 / 2.38 ( 218) hydrogen bonds : angle 4.46395 / 3.06 ( 615) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.282 Fit side-chains REVERT: A 102 ASP cc_start: 0.7763 (m-30) cc_final: 0.7361 (m-30) REVERT: A 225 GLN cc_start: 0.8253 (pm20) cc_final: 0.8047 (pm20) REVERT: B 302 TYR cc_start: 0.6666 (OUTLIER) cc_final: 0.5783 (t80) REVERT: D 97 ASN cc_start: 0.8138 (t0) cc_final: 0.7847 (t0) outliers start: 14 outliers final: 9 residues processed: 131 average time/residue: 0.0773 time to fit residues: 13.9693 Evaluate side-chains 132 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 449 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.139822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.111796 restraints weight = 11408.437| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.68 r_work: 0.3367 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7002 Z= 0.124 Angle : 0.587 15.907 9430 Z= 0.297 Chirality : 0.041 0.158 1009 Planarity : 0.004 0.052 1218 Dihedral : 5.263 46.634 938 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 1.68 % Allowed : 18.46 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.29), residues: 837 helix: -0.62 (0.29), residues: 327 sheet: -2.63 (0.43), residues: 127 loop : -1.87 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.009 0.001 TYR B 225 PHE 0.009 0.001 PHE B 78 TRP 0.005 0.001 TRP A 214 HIS 0.005 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.12 ( 7002) covalent geometry : angle 0.58717 / 0.30 ( 9430) hydrogen bonds : bond 0.03073 / 1.97 ( 218) hydrogen bonds : angle 4.31245 / 2.94 ( 615) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.272 Fit side-chains REVERT: A 102 ASP cc_start: 0.7747 (m-30) cc_final: 0.7365 (m-30) REVERT: A 135 ASP cc_start: 0.6863 (p0) cc_final: 0.6262 (t70) REVERT: A 225 GLN cc_start: 0.8176 (pm20) cc_final: 0.7972 (pm20) REVERT: B 129 MET cc_start: 0.8418 (ttm) cc_final: 0.8217 (ttp) REVERT: B 302 TYR cc_start: 0.6505 (OUTLIER) cc_final: 0.5657 (t80) REVERT: B 336 ASP cc_start: 0.8236 (t0) cc_final: 0.7930 (t0) REVERT: D 97 ASN cc_start: 0.8114 (t0) cc_final: 0.7819 (t0) outliers start: 12 outliers final: 9 residues processed: 130 average time/residue: 0.0779 time to fit residues: 14.0360 Evaluate side-chains 130 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 449 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.139640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.111780 restraints weight = 11357.082| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.68 r_work: 0.3368 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7002 Z= 0.129 Angle : 0.588 15.183 9430 Z= 0.299 Chirality : 0.042 0.216 1009 Planarity : 0.004 0.053 1218 Dihedral : 5.222 46.443 938 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 1.40 % Allowed : 18.46 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.29), residues: 837 helix: -0.60 (0.29), residues: 327 sheet: -2.62 (0.43), residues: 127 loop : -1.83 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 122 TYR 0.009 0.001 TYR D 138 PHE 0.010 0.001 PHE B 233 TRP 0.004 0.001 TRP B 261 HIS 0.004 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 7002) covalent geometry : angle 0.58809 / 0.30 ( 9430) hydrogen bonds : bond 0.02980 / 1.92 ( 218) hydrogen bonds : angle 4.26922 / 2.90 ( 615) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.292 Fit side-chains REVERT: A 102 ASP cc_start: 0.7713 (m-30) cc_final: 0.7343 (m-30) REVERT: A 135 ASP cc_start: 0.6817 (p0) cc_final: 0.6202 (t70) REVERT: A 222 MET cc_start: 0.8538 (mmm) cc_final: 0.8260 (mmm) REVERT: B 302 TYR cc_start: 0.6475 (OUTLIER) cc_final: 0.5619 (t80) REVERT: B 336 ASP cc_start: 0.8248 (t0) cc_final: 0.7946 (t0) REVERT: D 97 ASN cc_start: 0.8126 (t0) cc_final: 0.7816 (t0) REVERT: D 112 LEU cc_start: 0.8531 (mt) cc_final: 0.8273 (mt) outliers start: 10 outliers final: 9 residues processed: 132 average time/residue: 0.0714 time to fit residues: 12.9935 Evaluate side-chains 133 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 449 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.141115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.114670 restraints weight = 11297.304| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.58 r_work: 0.3429 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7002 Z= 0.116 Angle : 0.590 16.635 9430 Z= 0.298 Chirality : 0.041 0.206 1009 Planarity : 0.004 0.052 1218 Dihedral : 5.119 46.249 938 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.48 % Favored : 91.40 % Rotamer: Outliers : 1.40 % Allowed : 18.74 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.29), residues: 837 helix: -0.48 (0.29), residues: 328 sheet: -2.52 (0.44), residues: 127 loop : -1.77 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 122 TYR 0.008 0.001 TYR B 225 PHE 0.008 0.001 PHE B 78 TRP 0.005 0.001 TRP C 214 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 7002) covalent geometry : angle 0.58980 / 0.30 ( 9430) hydrogen bonds : bond 0.02774 / 1.79 ( 218) hydrogen bonds : angle 4.23629 / 2.88 ( 615) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.251 Fit side-chains REVERT: A 102 ASP cc_start: 0.7722 (m-30) cc_final: 0.7370 (m-30) REVERT: A 135 ASP cc_start: 0.6818 (p0) cc_final: 0.6178 (t70) REVERT: B 302 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.5660 (t80) REVERT: B 336 ASP cc_start: 0.8189 (t0) cc_final: 0.7924 (t0) REVERT: D 97 ASN cc_start: 0.8034 (t0) cc_final: 0.7728 (t0) REVERT: D 112 LEU cc_start: 0.8497 (mt) cc_final: 0.8252 (mt) outliers start: 10 outliers final: 5 residues processed: 129 average time/residue: 0.0742 time to fit residues: 13.3420 Evaluate side-chains 129 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 302 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 6 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.136625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109514 restraints weight = 11582.525| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.58 r_work: 0.3360 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7002 Z= 0.258 Angle : 0.712 15.725 9430 Z= 0.364 Chirality : 0.047 0.214 1009 Planarity : 0.005 0.054 1218 Dihedral : 5.798 47.702 938 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.75 % Favored : 89.13 % Rotamer: Outliers : 0.98 % Allowed : 19.30 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.28), residues: 837 helix: -0.89 (0.27), residues: 325 sheet: -2.88 (0.42), residues: 130 loop : -2.03 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 260 TYR 0.013 0.002 TYR A 197 PHE 0.020 0.002 PHE B 78 TRP 0.012 0.001 TRP A 214 HIS 0.013 0.002 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.26 ( 7002) covalent geometry : angle 0.71227 / 0.36 ( 9430) hydrogen bonds : bond 0.04166 / 2.72 ( 218) hydrogen bonds : angle 4.62349 / 3.16 ( 615) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1614.98 seconds wall clock time: 28 minutes 33.54 seconds (1713.54 seconds total)