Starting phenix.real_space_refine on Tue Sep 24 06:10:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8up1_42442/09_2024/8up1_42442.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8up1_42442/09_2024/8up1_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8up1_42442/09_2024/8up1_42442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8up1_42442/09_2024/8up1_42442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8up1_42442/09_2024/8up1_42442.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8up1_42442/09_2024/8up1_42442.cif" } resolution = 4.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 17, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 6, 'GLU:plan': 48, 'ARG:plan': 15} 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: {'GLN:plan1': 17, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 6, 'GLU:plan': 48, 'ARG:plan': 15} 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: {'GLN:plan1': 17, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 6, 'GLU:plan': 48, 'ARG:plan': 15} 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: {'GLN:plan1': 17, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 13, 'PHE:plan': 6, 'GLU:plan': 48, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 521 Time building chain proxies: 5.23, per 1000 atoms: 0.74 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: 1.89 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.81 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: 2.46 Time building geometry restraints manager: 2.17 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: 0.00 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.170 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.260 ------------------------------------------------------------------------------- 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= 0.646 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (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 TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** 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 fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.164 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0595 time to fit residues: 0.5681 Evaluate side-chains 4 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.8081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.026 7084 Z= 0.549 Angle : 0.952 10.491 9880 Z= 0.681 Chirality : 0.040 0.129 1376 Planarity : 0.005 0.022 1424 Dihedral : 6.972 35.284 1424 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 1.13 % Allowed : 3.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.21), residues: 1420 helix: 1.63 (0.14), residues: 1092 sheet: -0.02 (0.38), residues: 132 loop : -2.85 (0.37), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** 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 fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.190 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0212 time to fit residues: 0.4583 Evaluate side-chains 4 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.8309 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= 0.384 Angle : 0.778 10.451 9880 Z= 0.550 Chirality : 0.038 0.115 1376 Planarity : 0.003 0.019 1424 Dihedral : 6.203 34.314 1424 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.21), residues: 1420 helix: 2.51 (0.14), residues: 1084 sheet: -0.57 (0.44), residues: 108 loop : -2.90 (0.32), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** 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 fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.176 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0194 time to fit residues: 0.4350 Evaluate side-chains 4 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.8681 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= 0.446 Angle : 0.815 10.709 9880 Z= 0.587 Chirality : 0.038 0.117 1376 Planarity : 0.004 0.024 1424 Dihedral : 6.144 29.418 1424 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.51 % Favored : 95.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1420 helix: 1.56 (0.14), residues: 1072 sheet: -1.39 (0.43), residues: 104 loop : -3.16 (0.31), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** REFINEMENT MACRO_CYCLE 4 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 fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.190 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0201 time to fit residues: 0.4387 Evaluate side-chains 4 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.8985 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= 0.456 Angle : 0.817 11.122 9880 Z= 0.590 Chirality : 0.038 0.119 1376 Planarity : 0.004 0.025 1424 Dihedral : 6.055 32.354 1424 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1420 helix: 1.47 (0.14), residues: 1072 sheet: -0.88 (0.46), residues: 84 loop : -3.61 (0.30), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** REFINEMENT MACRO_CYCLE 5 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 fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.185 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0201 time to fit residues: 0.4336 Evaluate side-chains 4 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.8985 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= 0.422 Angle : 0.799 11.049 9880 Z= 0.574 Chirality : 0.038 0.117 1376 Planarity : 0.004 0.024 1424 Dihedral : 6.061 32.574 1424 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1420 helix: 1.44 (0.14), residues: 1072 sheet: -0.95 (0.46), residues: 84 loop : -3.65 (0.30), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** REFINEMENT MACRO_CYCLE 6 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 fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.187 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0205 time to fit residues: 0.4409 Evaluate side-chains 4 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 0.0040 chunk 83 optimal weight: 0.4980 overall best weight: 2.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.8964 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= 0.261 Angle : 0.697 10.341 9880 Z= 0.481 Chirality : 0.038 0.110 1376 Planarity : 0.003 0.024 1424 Dihedral : 5.418 32.943 1424 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.22), residues: 1420 helix: 2.86 (0.14), residues: 1076 sheet: -0.11 (0.48), residues: 80 loop : -3.69 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** REFINEMENT MACRO_CYCLE 7 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 fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.185 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0207 time to fit residues: 0.4429 Evaluate side-chains 4 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.9140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7084 Z= 0.326 Angle : 0.735 10.661 9880 Z= 0.516 Chirality : 0.038 0.115 1376 Planarity : 0.003 0.024 1424 Dihedral : 5.500 31.906 1424 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.22), residues: 1420 helix: 2.79 (0.14), residues: 1072 sheet: -0.09 (0.48), residues: 80 loop : -3.73 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** REFINEMENT MACRO_CYCLE 8 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 fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.192 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0204 time to fit residues: 0.4342 Evaluate side-chains 4 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 118 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.9319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7084 Z= 0.323 Angle : 0.724 10.509 9880 Z= 0.510 Chirality : 0.038 0.114 1376 Planarity : 0.003 0.023 1424 Dihedral : 5.365 31.340 1424 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.22), residues: 1420 helix: 2.86 (0.14), residues: 1072 sheet: -0.10 (0.46), residues: 80 loop : -3.76 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 *********************** REFINEMENT MACRO_CYCLE 9 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 fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.188 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0205 time to fit residues: 0.4469 Evaluate side-chains 4 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.9319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7084 Z= 0.311 Angle : 0.722 10.515 9880 Z= 0.507 Chirality : 0.038 0.111 1376 Planarity : 0.003 0.024 1424 Dihedral : 5.371 31.362 1424 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.22), residues: 1420 helix: 2.86 (0.14), residues: 1072 sheet: -0.11 (0.46), residues: 80 loop : -3.77 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 ********************** REFINEMENT MACRO_CYCLE 10 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 fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.190 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0211 time to fit residues: 0.4397 Evaluate side-chains 4 residues out of total 301 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 6 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 = 0.3393 r_free = 0.3393 target = 0.077074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.047875 restraints weight = 5793.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.048021 restraints weight = 5656.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.048188 restraints weight = 5544.408| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.9591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 7084 Z= 0.381 Angle : 0.768 11.012 9880 Z= 0.545 Chirality : 0.037 0.119 1376 Planarity : 0.004 0.025 1424 Dihedral : 5.641 32.547 1424 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.21), residues: 1420 helix: 2.43 (0.14), residues: 1072 sheet: -0.43 (0.44), residues: 80 loop : -3.81 (0.30), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 222 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1147.07 seconds wall clock time: 20 minutes 56.96 seconds (1256.96 seconds total)