Starting phenix.real_space_refine on Wed Mar 12 03:11:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8up1_42442/03_2025/8up1_42442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8up1_42442/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8up1_42442/03_2025/8up1_42442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8up1_42442/03_2025/8up1_42442.map" model { file = "/net/cci-nas-00/data/ceres_data/8up1_42442/03_2025/8up1_42442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8up1_42442/03_2025/8up1_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-5624/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: 5.74, per 1000 atoms: 0.81 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: 2.12 Conformation dependent library (CDL) restraints added in 1.3 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: 0.84 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: 2.70 Time building geometry restraints manager: 2.43 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: 0.03 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: 3.330 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: 0.050 Set scattering table: 0.070 Process input model: 22.970 Find NCS groups from input model: 0.260 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.980 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.209 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0380 time to fit residues: 0.5382 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 : 0.152 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.091722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.054693 restraints weight = 5206.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.054693 restraints weight = 5174.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.054693 restraints weight = 5174.229| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 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 to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.167 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0196 time to fit residues: 0.4064 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 : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 30 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 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 = 0.3542 r_free = 0.3542 target = 0.087244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.054358 restraints weight = 5680.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.054717 restraints weight = 5398.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.054924 restraints weight = 5202.743| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.8340 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= 0.388 Angle : 0.785 10.523 9880 Z= 0.554 Chirality : 0.038 0.112 1376 Planarity : 0.003 0.019 1424 Dihedral : 6.225 34.621 1424 Min Nonbonded Distance : 2.001 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: 2.21 (0.21), residues: 1420 helix: 2.51 (0.14), residues: 1084 sheet: -0.63 (0.44), residues: 108 loop : -2.93 (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 to be fit. 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: 0.0207 time to fit residues: 0.4511 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 : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 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 = 0.3409 r_free = 0.3409 target = 0.078232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.048611 restraints weight = 5743.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.048610 restraints weight = 5772.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.048610 restraints weight = 5772.189| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.8576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.023 7084 Z= 0.407 Angle : 0.783 10.559 9880 Z= 0.561 Chirality : 0.038 0.116 1376 Planarity : 0.004 0.024 1424 Dihedral : 5.933 28.407 1424 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % 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: 1.50 (0.21), residues: 1420 helix: 2.02 (0.14), residues: 1076 sheet: -1.36 (0.41), residues: 108 loop : -2.80 (0.34), residues: 236 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) ************************************************ 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 : 0.175 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0197 time to fit residues: 0.4096 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 : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 119 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.080109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.050544 restraints weight = 5834.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.050544 restraints weight = 5637.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.050544 restraints weight = 5637.058| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.8844 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= 0.351 Angle : 0.747 10.848 9880 Z= 0.527 Chirality : 0.038 0.110 1376 Planarity : 0.004 0.023 1424 Dihedral : 5.609 32.897 1424 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.48 % 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: 1.22 (0.21), residues: 1420 helix: 1.91 (0.14), residues: 1072 sheet: -0.75 (0.47), residues: 84 loop : -3.48 (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) ************************************************ 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 : 0.177 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0204 time to fit residues: 0.4334 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 : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 83 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.078689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.048259 restraints weight = 5985.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.048311 restraints weight = 5937.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.048342 restraints weight = 5906.020| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.9126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 7084 Z= 0.358 Angle : 0.750 10.773 9880 Z= 0.531 Chirality : 0.038 0.115 1376 Planarity : 0.004 0.023 1424 Dihedral : 5.596 30.027 1424 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % 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 (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: 1.06 (0.21), residues: 1420 helix: 1.83 (0.14), residues: 1076 sheet: -0.52 (0.44), residues: 80 loop : -3.84 (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) ************************************************ 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 : 0.186 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0205 time to fit residues: 0.4420 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 : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 130 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 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 = 0.3370 r_free = 0.3370 target = 0.075992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.047084 restraints weight = 5898.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.047104 restraints weight = 5883.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.047104 restraints weight = 5872.465| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.9544 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= 0.420 Angle : 0.800 11.234 9880 Z= 0.572 Chirality : 0.038 0.120 1376 Planarity : 0.004 0.025 1424 Dihedral : 5.911 33.064 1424 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.29 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 : 0.57 % 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: -0.13 (0.20), residues: 1420 helix: 0.95 (0.14), residues: 1072 sheet: -1.05 (0.41), residues: 80 loop : -4.01 (0.28), 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 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 : 0.184 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0203 time to fit residues: 0.4260 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 : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 69 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.076107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.047785 restraints weight = 5952.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.047785 restraints weight = 5840.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.047785 restraints weight = 5840.261| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.9544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 7084 Z= 0.399 Angle : 0.791 11.183 9880 Z= 0.563 Chirality : 0.037 0.119 1376 Planarity : 0.004 0.024 1424 Dihedral : 5.934 33.223 1424 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.39 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 : 0.57 % 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: -0.18 (0.20), residues: 1420 helix: 0.90 (0.14), residues: 1072 sheet: -1.09 (0.41), residues: 80 loop : -4.01 (0.28), 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) ************************************************ 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 : 0.173 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0196 time to fit residues: 0.4273 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 : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 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 = 0.3374 r_free = 0.3374 target = 0.076163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.047113 restraints weight = 5793.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.047312 restraints weight = 5595.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.047312 restraints weight = 5452.880| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.9550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 7084 Z= 0.397 Angle : 0.781 11.156 9880 Z= 0.557 Chirality : 0.038 0.118 1376 Planarity : 0.004 0.023 1424 Dihedral : 5.924 33.234 1424 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.29 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 : 0.57 % 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: -0.20 (0.20), residues: 1420 helix: 0.91 (0.14), residues: 1072 sheet: -1.20 (0.40), residues: 80 loop : -4.05 (0.29), 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) ************************************************ 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 : 0.186 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0223 time to fit residues: 0.4662 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 : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 2 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.076599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.047350 restraints weight = 5947.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.047350 restraints weight = 5739.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.047350 restraints weight = 5739.153| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.9549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 7084 Z= 0.366 Angle : 0.772 11.135 9880 Z= 0.547 Chirality : 0.038 0.116 1376 Planarity : 0.004 0.023 1424 Dihedral : 5.936 33.182 1424 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.29 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 : 0.57 % 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: -0.20 (0.20), residues: 1420 helix: 0.91 (0.14), residues: 1072 sheet: -1.20 (0.40), residues: 80 loop : -4.06 (0.29), 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) ************************************************ 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 : 0.170 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0192 time to fit residues: 0.4263 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 : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 6 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 103 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 = 0.3377 r_free = 0.3377 target = 0.076397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.047221 restraints weight = 5788.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.047411 restraints weight = 5624.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.047411 restraints weight = 5501.513| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.9590 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= 0.402 Angle : 0.780 10.998 9880 Z= 0.556 Chirality : 0.037 0.118 1376 Planarity : 0.004 0.024 1424 Dihedral : 5.861 32.700 1424 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.29 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 : 0.57 % 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: -0.18 (0.20), residues: 1420 helix: 0.94 (0.14), residues: 1072 sheet: -1.47 (0.38), residues: 80 loop : -4.03 (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: 1346.21 seconds wall clock time: 23 minutes 57.77 seconds (1437.77 seconds total)