Starting phenix.real_space_refine on Fri Aug 22 19:13:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8up1_42442/08_2025/8up1_42442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8up1_42442/08_2025/8up1_42442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8up1_42442/08_2025/8up1_42442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8up1_42442/08_2025/8up1_42442.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8up1_42442/08_2025/8up1_42442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8up1_42442/08_2025/8up1_42442.map" } resolution = 4.55 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= 0.001 sd= 0.027 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: 3 Type Number sf(0) Gaussians C 4232 2.51 5 N 1428 2.21 5 O 1428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7088 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 1772 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 301} Link IDs: {'PTRANS': 6, 'TRANS': 350} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1051 Unresolved non-hydrogen angles: 1338 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'PHE:plan': 6, 'ASP:plan': 13, 'ASN:plan1': 4, 'HIS:plan': 13, 'GLU:plan': 48, 'ARG:plan': 15, 'GLN:plan1': 17, 'TRP:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 521 Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 1772 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 301} Link IDs: {'PTRANS': 6, 'TRANS': 350} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1051 Unresolved non-hydrogen angles: 1338 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'PHE:plan': 6, 'ASP:plan': 13, 'ASN:plan1': 4, 'HIS:plan': 13, 'GLU:plan': 48, 'ARG:plan': 15, 'GLN:plan1': 17, 'TRP:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 521 Chain: "C" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 1772 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 301} Link IDs: {'PTRANS': 6, 'TRANS': 350} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1051 Unresolved non-hydrogen angles: 1338 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'PHE:plan': 6, 'ASP:plan': 13, 'ASN:plan1': 4, 'HIS:plan': 13, 'GLU:plan': 48, 'ARG:plan': 15, 'GLN:plan1': 17, 'TRP:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 521 Chain: "D" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 1772 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 301} Link IDs: {'PTRANS': 6, 'TRANS': 350} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 1051 Unresolved non-hydrogen angles: 1338 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'PHE:plan': 6, 'ASP:plan': 13, 'ASN:plan1': 4, 'HIS:plan': 13, 'GLU:plan': 48, 'ARG:plan': 15, 'GLN:plan1': 17, 'TRP:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 521 Time building chain proxies: 2.30, per 1000 atoms: 0.32 Number of scatterers: 7088 At special positions: 0 Unit cell: (128.52, 127.68, 66.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1428 8.00 N 1428 7.00 C 4232 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: 0.65 Conformation dependent library (CDL) restraints added in 522.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 77.0% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 10 through 27 Processing helix chain 'A' and resid 49 through 67 removed outlier: 3.737A pdb=" N ASP A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 88 Processing helix chain 'A' and resid 90 through 105 removed outlier: 3.800A pdb=" N ILE A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 133 Processing helix chain 'A' and resid 134 through 161 removed outlier: 4.046A pdb=" N ALA A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 191 Processing helix chain 'A' and resid 194 through 227 removed outlier: 4.043A pdb=" N ALA A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 254 Processing helix chain 'A' and resid 275 through 294 removed outlier: 4.080A pdb=" N ARG A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 334 removed outlier: 4.006A pdb=" N LYS A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'B' and resid 10 through 24 removed outlier: 3.713A pdb=" N ILE B 16 " --> pdb=" O LYS B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 49 through 67 removed outlier: 4.033A pdb=" N ASP B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 88 Processing helix chain 'B' and resid 90 through 108 removed outlier: 3.755A pdb=" N ILE B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU B 103 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 133 Processing helix chain 'B' and resid 134 through 161 removed outlier: 3.990A pdb=" N ALA B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 191 removed outlier: 3.566A pdb=" N LEU B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 227 removed outlier: 3.759A pdb=" N ALA B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 254 Processing helix chain 'B' and resid 275 through 294 Processing helix chain 'B' and resid 317 through 334 removed outlier: 3.568A pdb=" N GLU B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'C' and resid 10 through 26 Processing helix chain 'C' and resid 49 through 67 removed outlier: 4.041A pdb=" N ASP C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 Processing helix chain 'C' and resid 90 through 108 removed outlier: 3.655A pdb=" N ILE C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU C 103 " --> pdb=" O LYS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 133 Processing helix chain 'C' and resid 134 through 161 Processing helix chain 'C' and resid 164 through 191 Processing helix chain 'C' and resid 194 through 227 removed outlier: 4.039A pdb=" N ALA C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 203 " --> pdb=" O LYS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 255 removed outlier: 3.835A pdb=" N MET C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 294 removed outlier: 4.561A pdb=" N GLN C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 333 removed outlier: 4.364A pdb=" N GLU C 321 " --> pdb=" O GLU C 317 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 338 through 354 removed outlier: 3.624A pdb=" N GLU C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 49 through 67 Processing helix chain 'D' and resid 70 through 88 Processing helix chain 'D' and resid 90 through 108 removed outlier: 3.845A pdb=" N LEU D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 133 removed outlier: 4.339A pdb=" N LYS D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 161 Processing helix chain 'D' and resid 164 through 191 Processing helix chain 'D' and resid 194 through 227 removed outlier: 3.782A pdb=" N ALA D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 255 Processing helix chain 'D' and resid 275 through 294 Processing helix chain 'D' and resid 315 through 333 removed outlier: 4.245A pdb=" N GLU D 321 " --> pdb=" O GLU D 317 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'D' and resid 353 through 357 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 4.053A pdb=" N ILE B 299 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR B 257 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 262 removed outlier: 3.867A pdb=" N ILE A 305 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU A 297 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER D 36 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 4.180A pdb=" N THR C 257 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 2 through 6 removed outlier: 3.558A pdb=" N SER C 36 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR D 257 " --> pdb=" O LEU D 272 " (cutoff:3.500A) 992 hydrogen bonds defined for protein. 2910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 1428 1.28 - 1.35: 1424 1.35 - 1.42: 0 1.42 - 1.49: 1426 1.49 - 1.55: 2806 Bond restraints: 7084 Sorted by residual: bond pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.18e-02 7.18e+03 9.06e+00 bond pdb=" CA ASP A 134 " pdb=" C ASP A 134 " ideal model delta sigma weight residual 1.519 1.547 -0.029 1.15e-02 7.56e+03 6.24e+00 bond pdb=" CA ASP C 70 " pdb=" C ASP C 70 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.19e-02 7.06e+03 5.41e+00 bond pdb=" CA HIS C 161 " pdb=" C HIS C 161 " ideal model delta sigma weight residual 1.524 1.552 -0.028 1.26e-02 6.30e+03 4.97e+00 bond pdb=" CA ASP A 70 " pdb=" C ASP A 70 " ideal model delta sigma weight residual 1.523 1.549 -0.026 1.19e-02 7.06e+03 4.74e+00 ... (remaining 7079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 7649 1.70 - 3.40: 1928 3.40 - 5.10: 285 5.10 - 6.80: 17 6.80 - 8.50: 1 Bond angle restraints: 9880 Sorted by residual: angle pdb=" C SER A 36 " pdb=" N GLU A 37 " pdb=" CA GLU A 37 " ideal model delta sigma weight residual 121.80 130.30 -8.50 1.71e+00 3.42e-01 2.47e+01 angle pdb=" N ARG C 334 " pdb=" CA ARG C 334 " pdb=" C ARG C 334 " ideal model delta sigma weight residual 111.71 117.17 -5.46 1.15e+00 7.56e-01 2.25e+01 angle pdb=" C MET C 188 " pdb=" N LEU C 189 " pdb=" CA LEU C 189 " ideal model delta sigma weight residual 120.28 126.14 -5.86 1.34e+00 5.57e-01 1.91e+01 angle pdb=" N ARG A 334 " pdb=" CA ARG A 334 " pdb=" C ARG A 334 " ideal model delta sigma weight residual 111.28 115.94 -4.66 1.09e+00 8.42e-01 1.83e+01 angle pdb=" C THR A 338 " pdb=" N GLU A 339 " pdb=" CA GLU A 339 " ideal model delta sigma weight residual 120.28 125.98 -5.70 1.34e+00 5.57e-01 1.81e+01 ... (remaining 9875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.79: 3597 5.79 - 11.59: 458 11.59 - 17.38: 97 17.38 - 23.17: 16 23.17 - 28.96: 8 Dihedral angle restraints: 4176 sinusoidal: 0 harmonic: 4176 Sorted by residual: dihedral pdb=" CA LEU C 297 " pdb=" C LEU C 297 " pdb=" N SER C 298 " pdb=" CA SER C 298 " ideal model delta harmonic sigma weight residual 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA LEU A 297 " pdb=" C LEU A 297 " pdb=" N SER A 298 " pdb=" CA SER A 298 " ideal model delta harmonic sigma weight residual 180.00 151.16 28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA LEU D 297 " pdb=" C LEU D 297 " pdb=" N SER D 298 " pdb=" CA SER D 298 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 4173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 988 0.061 - 0.122: 298 0.122 - 0.182: 68 0.182 - 0.243: 20 0.243 - 0.304: 2 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CA ASN B 193 " pdb=" N ASN B 193 " pdb=" C ASN B 193 " pdb=" CB ASN B 193 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA ASN B 8 " pdb=" N ASN B 8 " pdb=" C ASN B 8 " pdb=" CB ASN B 8 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ASN D 47 " pdb=" N ASN D 47 " pdb=" C ASN D 47 " pdb=" CB ASN D 47 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1373 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 148 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C GLU B 148 " 0.042 2.00e-02 2.50e+03 pdb=" O GLU B 148 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 149 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 297 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C LEU A 297 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU A 297 " 0.015 2.00e-02 2.50e+03 pdb=" N SER A 298 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 151 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C VAL A 151 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL A 151 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG A 152 " -0.013 2.00e-02 2.50e+03 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.06: 4784 3.06 - 3.52: 9072 3.52 - 3.98: 8735 3.98 - 4.44: 10476 4.44 - 4.90: 15713 Nonbonded interactions: 48780 Sorted by model distance: nonbonded pdb=" N GLU A 37 " pdb=" O GLU A 37 " model vdw 2.606 2.496 nonbonded pdb=" N ALA C 314 " pdb=" O ALA C 314 " model vdw 2.640 2.496 nonbonded pdb=" N GLU C 37 " pdb=" O GLU C 37 " model vdw 2.654 2.496 nonbonded pdb=" O VAL B 150 " pdb=" CA VAL B 151 " model vdw 2.657 2.776 nonbonded pdb=" N LEU A 108 " pdb=" O LEU A 108 " model vdw 2.657 2.496 ... (remaining 48775 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.490 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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 : 0.009 0.036 7084 Z= 0.684 Angle : 1.485 8.504 9880 Z= 1.077 Chirality : 0.065 0.304 1376 Planarity : 0.010 0.025 1424 Dihedral : 6.866 28.962 1424 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: 0.31 (0.19), residues: 1420 helix: 0.46 (0.14), residues: 1052 sheet: 0.81 (0.40), residues: 130 loop : -0.73 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00892 ( 7084) covalent geometry : angle 1.48458 ( 9880) hydrogen bonds : bond 0.13103 ( 992) hydrogen bonds : angle 6.33166 ( 2910) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.058 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0143 time to fit residues: 0.1751 Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.094807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.057610 restraints weight = 5138.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.057609 restraints weight = 5159.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.057609 restraints weight = 5159.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.057609 restraints weight = 5159.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.057609 restraints weight = 5159.591| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.8041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 7084 Z= 0.437 Angle : 0.864 9.435 9880 Z= 0.602 Chirality : 0.039 0.120 1376 Planarity : 0.004 0.024 1424 Dihedral : 6.630 34.729 1424 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.85 % Allowed : 3.66 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.86 % 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 aren not related in a simple way. whole: 2.56 (0.21), residues: 1420 helix: 2.54 (0.14), residues: 1092 sheet: 0.51 (0.40), residues: 132 loop : -2.64 (0.38), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 7084) covalent geometry : angle 0.86443 ( 9880) hydrogen bonds : bond 0.13231 ( 992) hydrogen bonds : angle 8.24689 ( 2910) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.062 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0096 time to fit residues: 0.1649 Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 65 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 99 optimal weight: 4.9990 chunk 16 optimal weight: 0.0770 chunk 91 optimal weight: 3.9990 overall best weight: 2.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.092825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.058566 restraints weight = 5788.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.058836 restraints weight = 5573.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.058836 restraints weight = 5428.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.058836 restraints weight = 5427.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.058836 restraints weight = 5427.734| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.8257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 7084 Z= 0.286 Angle : 0.705 9.831 9880 Z= 0.486 Chirality : 0.038 0.111 1376 Planarity : 0.003 0.017 1424 Dihedral : 5.718 32.568 1424 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 aren not related in a simple way. whole: 3.76 (0.21), residues: 1420 helix: 3.67 (0.14), residues: 1088 sheet: -0.17 (0.45), residues: 112 loop : -2.81 (0.34), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 7084) covalent geometry : angle 0.70533 ( 9880) hydrogen bonds : bond 0.11249 ( 992) hydrogen bonds : angle 7.60179 ( 2910) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.063 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0099 time to fit residues: 0.1662 Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 25 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.080793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.050162 restraints weight = 5935.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.050162 restraints weight = 5884.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.050162 restraints weight = 5884.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.050162 restraints weight = 5884.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.050162 restraints weight = 5884.775| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.8394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 7084 Z= 0.381 Angle : 0.751 10.379 9880 Z= 0.532 Chirality : 0.038 0.112 1376 Planarity : 0.004 0.024 1424 Dihedral : 5.567 28.621 1424 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: 2.36 (0.21), residues: 1420 helix: 2.68 (0.14), residues: 1084 sheet: -0.96 (0.43), residues: 108 loop : -3.05 (0.32), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 7084) covalent geometry : angle 0.75066 ( 9880) hydrogen bonds : bond 0.11734 ( 992) hydrogen bonds : angle 7.85384 ( 2910) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.066 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0101 time to fit residues: 0.1779 Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 35 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.083338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.052182 restraints weight = 5957.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.052181 restraints weight = 5944.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.052179 restraints weight = 5945.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.052179 restraints weight = 5945.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.052179 restraints weight = 5945.908| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.8570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 7084 Z= 0.301 Angle : 0.695 10.170 9880 Z= 0.483 Chirality : 0.038 0.107 1376 Planarity : 0.003 0.023 1424 Dihedral : 5.151 30.362 1424 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 aren not related in a simple way. whole: 2.50 (0.21), residues: 1420 helix: 2.85 (0.14), residues: 1084 sheet: 0.32 (0.42), residues: 80 loop : -3.63 (0.31), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 7084) covalent geometry : angle 0.69517 ( 9880) hydrogen bonds : bond 0.10804 ( 992) hydrogen bonds : angle 7.62527 ( 2910) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.041 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0068 time to fit residues: 0.1256 Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 91 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.078199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.047950 restraints weight = 5916.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.047950 restraints weight = 5891.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.047950 restraints weight = 5891.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.047950 restraints weight = 5891.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.047950 restraints weight = 5891.868| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.8795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.024 7084 Z= 0.436 Angle : 0.779 10.894 9880 Z= 0.557 Chirality : 0.038 0.115 1376 Planarity : 0.004 0.024 1424 Dihedral : 5.658 31.496 1424 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.04 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 aren not related in a simple way. whole: 0.73 (0.21), residues: 1420 helix: 1.52 (0.14), residues: 1072 sheet: -0.49 (0.49), residues: 84 loop : -3.64 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 7084) covalent geometry : angle 0.77885 ( 9880) hydrogen bonds : bond 0.11962 ( 992) hydrogen bonds : angle 8.04433 ( 2910) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.062 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0080 time to fit residues: 0.1401 Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 93 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.078434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.047805 restraints weight = 5869.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.047805 restraints weight = 5809.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.047805 restraints weight = 5809.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.047805 restraints weight = 5809.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.047805 restraints weight = 5809.815| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.8795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 7084 Z= 0.412 Angle : 0.766 10.807 9880 Z= 0.545 Chirality : 0.038 0.115 1376 Planarity : 0.004 0.024 1424 Dihedral : 5.692 31.671 1424 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.32 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 aren not related in a simple way. whole: 0.64 (0.21), residues: 1420 helix: 1.45 (0.14), residues: 1072 sheet: -0.53 (0.49), residues: 84 loop : -3.68 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 7084) covalent geometry : angle 0.76639 ( 9880) hydrogen bonds : bond 0.11960 ( 992) hydrogen bonds : angle 8.04628 ( 2910) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.037 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0062 time to fit residues: 0.0990 Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 129 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.078896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.048426 restraints weight = 5924.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.048536 restraints weight = 5847.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.048599 restraints weight = 5783.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.048600 restraints weight = 5738.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.048600 restraints weight = 5737.642| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.8795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 7084 Z= 0.373 Angle : 0.755 10.786 9880 Z= 0.534 Chirality : 0.038 0.111 1376 Planarity : 0.004 0.024 1424 Dihedral : 5.713 31.763 1424 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.32 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 aren not related in a simple way. whole: 0.65 (0.21), residues: 1420 helix: 1.47 (0.14), residues: 1072 sheet: -0.53 (0.49), residues: 84 loop : -3.68 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 7084) covalent geometry : angle 0.75496 ( 9880) hydrogen bonds : bond 0.11917 ( 992) hydrogen bonds : angle 8.03650 ( 2910) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.062 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0095 time to fit residues: 0.1517 Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 4 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.078983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.048552 restraints weight = 5935.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.048552 restraints weight = 5832.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.048552 restraints weight = 5832.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.048552 restraints weight = 5832.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.048552 restraints weight = 5832.854| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.8795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 7084 Z= 0.372 Angle : 0.746 10.724 9880 Z= 0.525 Chirality : 0.038 0.115 1376 Planarity : 0.004 0.024 1424 Dihedral : 5.725 31.767 1424 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.32 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 aren not related in a simple way. whole: 0.64 (0.21), residues: 1420 helix: 1.46 (0.14), residues: 1072 sheet: -0.53 (0.49), residues: 84 loop : -3.69 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 7084) covalent geometry : angle 0.74598 ( 9880) hydrogen bonds : bond 0.11880 ( 992) hydrogen bonds : angle 8.01879 ( 2910) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.061 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0064 time to fit residues: 0.1133 Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 97 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.078053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.048307 restraints weight = 5901.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 11)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.048307 restraints weight = 5851.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.048307 restraints weight = 5851.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.048307 restraints weight = 5851.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.048307 restraints weight = 5851.059| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.8882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 7084 Z= 0.442 Angle : 0.777 10.852 9880 Z= 0.556 Chirality : 0.038 0.116 1376 Planarity : 0.004 0.024 1424 Dihedral : 5.885 32.774 1424 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.61 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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 aren not related in a simple way. whole: -0.05 (0.20), residues: 1420 helix: 0.98 (0.14), residues: 1076 sheet: -1.15 (0.44), residues: 84 loop : -3.95 (0.31), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00567 ( 7084) covalent geometry : angle 0.77683 ( 9880) hydrogen bonds : bond 0.12042 ( 992) hydrogen bonds : angle 8.11078 ( 2910) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.060 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0093 time to fit residues: 0.1558 Evaluate side-chains 4 residues out of total 301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 123 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.078646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.048344 restraints weight = 6033.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.048488 restraints weight = 5928.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 13)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.048488 restraints weight = 5834.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.048488 restraints weight = 5834.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.048488 restraints weight = 5834.321| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.8881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 7084 Z= 0.381 Angle : 0.761 10.774 9880 Z= 0.540 Chirality : 0.038 0.111 1376 Planarity : 0.004 0.024 1424 Dihedral : 5.918 32.871 1424 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.61 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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 aren not related in a simple way. whole: -0.09 (0.20), residues: 1420 helix: 0.96 (0.14), residues: 1076 sheet: -1.28 (0.43), residues: 84 loop : -3.97 (0.31), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 249 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 222 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 7084) covalent geometry : angle 0.76074 ( 9880) hydrogen bonds : bond 0.11981 ( 992) hydrogen bonds : angle 8.09376 ( 2910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 714.98 seconds wall clock time: 12 minutes 58.26 seconds (778.26 seconds total)