Starting phenix.real_space_refine on Sat Aug 23 10:43:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b78_44303/08_2025/9b78_44303.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b78_44303/08_2025/9b78_44303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b78_44303/08_2025/9b78_44303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b78_44303/08_2025/9b78_44303.map" model { file = "/net/cci-nas-00/data/ceres_data/9b78_44303/08_2025/9b78_44303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b78_44303/08_2025/9b78_44303.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 7440 2.51 5 N 2118 2.21 5 O 2214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11814 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1969 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "B" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1969 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "C" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1969 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "D" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1969 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "E" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1969 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "F" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1969 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Time building chain proxies: 3.07, per 1000 atoms: 0.26 Number of scatterers: 11814 At special positions: 0 Unit cell: (104.902, 108.206, 99.946, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2214 8.00 N 2118 7.00 C 7440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 601.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2868 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 46.4% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 20 through 24 Processing helix chain 'A' and resid 39 through 52 Processing helix chain 'A' and resid 53 through 56 removed outlier: 4.023A pdb=" N GLU A 56 " --> pdb=" O GLU A 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 53 through 56' Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 109 through 124 removed outlier: 3.527A pdb=" N ILE A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 167 Processing helix chain 'A' and resid 185 through 213 Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.525A pdb=" N LEU A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'B' and resid 20 through 24 removed outlier: 3.704A pdb=" N ALA B 24 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 52 Processing helix chain 'B' and resid 53 through 58 removed outlier: 3.800A pdb=" N GLU B 56 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 58 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 82 removed outlier: 3.735A pdb=" N TRP B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 124 Processing helix chain 'B' and resid 155 through 167 removed outlier: 3.619A pdb=" N SER B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 213 removed outlier: 3.752A pdb=" N PHE B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 3.760A pdb=" N LEU B 234 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'C' and resid 20 through 24 removed outlier: 3.707A pdb=" N ALA C 24 " --> pdb=" O LYS C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 52 Processing helix chain 'C' and resid 53 through 58 removed outlier: 4.152A pdb=" N GLU C 56 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 58 " --> pdb=" O SER C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 82 Processing helix chain 'C' and resid 109 through 124 removed outlier: 3.528A pdb=" N ILE C 113 " --> pdb=" O GLY C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 167 Processing helix chain 'C' and resid 185 through 212 removed outlier: 3.614A pdb=" N PHE C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 235 removed outlier: 3.510A pdb=" N LEU C 234 " --> pdb=" O THR C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 247 through 261 Processing helix chain 'D' and resid 20 through 24 Processing helix chain 'D' and resid 39 through 52 Processing helix chain 'D' and resid 53 through 58 removed outlier: 3.730A pdb=" N GLU D 56 " --> pdb=" O GLU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.904A pdb=" N TRP D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 124 Processing helix chain 'D' and resid 155 through 167 Processing helix chain 'D' and resid 185 through 213 removed outlier: 3.889A pdb=" N PHE D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 235 removed outlier: 3.932A pdb=" N LEU D 234 " --> pdb=" O THR D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 247 through 260 Processing helix chain 'E' and resid 20 through 24 Processing helix chain 'E' and resid 39 through 52 Processing helix chain 'E' and resid 53 through 58 removed outlier: 4.142A pdb=" N GLU E 56 " --> pdb=" O GLU E 53 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU E 58 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 82 Processing helix chain 'E' and resid 109 through 124 removed outlier: 3.565A pdb=" N ILE E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 167 Processing helix chain 'E' and resid 185 through 213 removed outlier: 4.034A pdb=" N PHE E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 235 removed outlier: 3.705A pdb=" N LEU E 234 " --> pdb=" O THR E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 238 No H-bonds generated for 'chain 'E' and resid 236 through 238' Processing helix chain 'E' and resid 247 through 260 Processing helix chain 'F' and resid 20 through 24 Processing helix chain 'F' and resid 39 through 52 Processing helix chain 'F' and resid 53 through 55 No H-bonds generated for 'chain 'F' and resid 53 through 55' Processing helix chain 'F' and resid 67 through 82 Processing helix chain 'F' and resid 109 through 124 removed outlier: 3.522A pdb=" N ILE F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 167 removed outlier: 3.523A pdb=" N SER F 159 " --> pdb=" O GLY F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 213 removed outlier: 3.862A pdb=" N PHE F 198 " --> pdb=" O ALA F 194 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL F 213 " --> pdb=" O ILE F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 235 removed outlier: 3.584A pdb=" N LEU F 234 " --> pdb=" O THR F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 238 No H-bonds generated for 'chain 'F' and resid 236 through 238' Processing helix chain 'F' and resid 247 through 260 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 33 removed outlier: 5.340A pdb=" N VAL A 26 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N SER A 18 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU A 3 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU A 64 " --> pdb=" O LEU A 3 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE A 5 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER A 65 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 154 removed outlier: 3.828A pdb=" N GLY A 149 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE A 224 " --> pdb=" O HIS A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 33 removed outlier: 5.472A pdb=" N VAL B 26 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER B 18 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU B 3 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU B 64 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE B 5 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR B 61 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILE B 90 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA B 63 " --> pdb=" O ILE B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 147 through 154 removed outlier: 3.969A pdb=" N GLY B 149 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE B 224 " --> pdb=" O HIS B 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 33 removed outlier: 5.495A pdb=" N VAL C 26 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER C 18 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR C 61 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE C 90 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA C 63 " --> pdb=" O ILE C 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 147 through 154 removed outlier: 4.090A pdb=" N GLY C 149 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N HIS C 243 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE C 224 " --> pdb=" O HIS C 243 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 25 through 33 removed outlier: 5.430A pdb=" N VAL D 26 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N SER D 18 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU D 3 " --> pdb=" O ALA D 62 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU D 64 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE D 5 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER D 65 " --> pdb=" O ILE D 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 147 through 154 removed outlier: 4.022A pdb=" N GLY D 149 " --> pdb=" O VAL D 140 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE D 224 " --> pdb=" O HIS D 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 25 through 33 removed outlier: 5.445A pdb=" N VAL E 26 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER E 18 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU E 3 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU E 64 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ILE E 5 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR E 61 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE E 90 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA E 63 " --> pdb=" O ILE E 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 147 through 154 removed outlier: 3.729A pdb=" N GLY E 149 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE E 224 " --> pdb=" O HIS E 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 25 through 33 removed outlier: 5.522A pdb=" N VAL F 26 " --> pdb=" O SER F 18 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER F 18 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU F 3 " --> pdb=" O ALA F 62 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU F 64 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE F 5 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR F 61 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE F 90 " --> pdb=" O THR F 61 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA F 63 " --> pdb=" O ILE F 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 147 through 154 removed outlier: 4.008A pdb=" N GLY F 149 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N HIS F 243 " --> pdb=" O VAL F 222 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE F 224 " --> pdb=" O HIS F 243 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4082 1.34 - 1.46: 2167 1.46 - 1.58: 5691 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 12006 Sorted by residual: bond pdb=" CB VAL B 114 " pdb=" CG1 VAL B 114 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.27e-01 bond pdb=" CB VAL F 114 " pdb=" CG1 VAL F 114 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.25e-01 bond pdb=" CB VAL A 114 " pdb=" CG1 VAL A 114 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.55e-01 bond pdb=" CB VAL D 114 " pdb=" CG1 VAL D 114 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.49e-01 bond pdb=" C ALA D 231 " pdb=" N PRO D 232 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.19e-02 7.06e+03 6.96e-01 ... (remaining 12001 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 15977 1.39 - 2.77: 297 2.77 - 4.16: 38 4.16 - 5.55: 21 5.55 - 6.93: 5 Bond angle restraints: 16338 Sorted by residual: angle pdb=" C GLY A 197 " pdb=" N PHE A 198 " pdb=" CA PHE A 198 " ideal model delta sigma weight residual 120.68 117.02 3.66 1.70e+00 3.46e-01 4.63e+00 angle pdb=" CA LEU F 201 " pdb=" CB LEU F 201 " pdb=" CG LEU F 201 " ideal model delta sigma weight residual 116.30 122.60 -6.30 3.50e+00 8.16e-02 3.24e+00 angle pdb=" CG1 VAL C 88 " pdb=" CB VAL C 88 " pdb=" CG2 VAL C 88 " ideal model delta sigma weight residual 110.80 106.88 3.92 2.20e+00 2.07e-01 3.17e+00 angle pdb=" N ASP E 212 " pdb=" CA ASP E 212 " pdb=" C ASP E 212 " ideal model delta sigma weight residual 113.16 115.35 -2.19 1.24e+00 6.50e-01 3.11e+00 angle pdb=" CA LEU C 201 " pdb=" CB LEU C 201 " pdb=" CG LEU C 201 " ideal model delta sigma weight residual 116.30 122.40 -6.10 3.50e+00 8.16e-02 3.04e+00 ... (remaining 16333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 6691 16.43 - 32.87: 417 32.87 - 49.30: 79 49.30 - 65.74: 9 65.74 - 82.17: 4 Dihedral angle restraints: 7200 sinusoidal: 2754 harmonic: 4446 Sorted by residual: dihedral pdb=" CA GLN D 80 " pdb=" C GLN D 80 " pdb=" N TYR D 81 " pdb=" CA TYR D 81 " ideal model delta harmonic sigma weight residual -180.00 -164.00 -16.00 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA GLU C 22 " pdb=" CB GLU C 22 " pdb=" CG GLU C 22 " pdb=" CD GLU C 22 " ideal model delta sinusoidal sigma weight residual -60.00 -116.82 56.82 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA LYS B 25 " pdb=" CB LYS B 25 " pdb=" CG LYS B 25 " pdb=" CD LYS B 25 " ideal model delta sinusoidal sigma weight residual 180.00 124.64 55.36 3 1.50e+01 4.44e-03 9.34e+00 ... (remaining 7197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1265 0.036 - 0.071: 468 0.071 - 0.107: 165 0.107 - 0.143: 75 0.143 - 0.178: 7 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CB VAL F 213 " pdb=" CA VAL F 213 " pdb=" CG1 VAL F 213 " pdb=" CG2 VAL F 213 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CB VAL A 213 " pdb=" CA VAL A 213 " pdb=" CG1 VAL A 213 " pdb=" CG2 VAL A 213 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB VAL E 213 " pdb=" CA VAL E 213 " pdb=" CG1 VAL E 213 " pdb=" CG2 VAL E 213 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.20e-01 ... (remaining 1977 not shown) Planarity restraints: 2118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 194 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ALA A 194 " 0.058 2.00e-02 2.50e+03 pdb=" O ALA A 194 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 195 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 193 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.05e+00 pdb=" C GLY B 193 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY B 193 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA B 194 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 193 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C GLY F 193 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY F 193 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA F 194 " 0.010 2.00e-02 2.50e+03 ... (remaining 2115 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2147 2.78 - 3.31: 10667 3.31 - 3.84: 20213 3.84 - 4.37: 23381 4.37 - 4.90: 41353 Nonbonded interactions: 97761 Sorted by model distance: nonbonded pdb=" O GLY C 155 " pdb=" OG SER C 159 " model vdw 2.252 3.040 nonbonded pdb=" OD1 ASP E 41 " pdb=" OH TYR E 81 " model vdw 2.256 3.040 nonbonded pdb=" OD1 ASP F 41 " pdb=" OH TYR F 81 " model vdw 2.272 3.040 nonbonded pdb=" OD1 ASP A 41 " pdb=" OH TYR A 81 " model vdw 2.275 3.040 nonbonded pdb=" O GLY A 155 " pdb=" OG SER A 159 " model vdw 2.289 3.040 ... (remaining 97756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.920 Find NCS groups from input model: 0.200 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:7.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.002 0.032 12006 Z= 0.114 Angle : 0.513 6.934 16338 Z= 0.272 Chirality : 0.046 0.178 1980 Planarity : 0.005 0.041 2118 Dihedral : 11.205 82.170 4332 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.20), residues: 1554 helix: 1.49 (0.21), residues: 582 sheet: 0.71 (0.30), residues: 294 loop : -1.03 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 75 TYR 0.006 0.001 TYR E 120 PHE 0.006 0.001 PHE F 198 TRP 0.014 0.002 TRP C 30 HIS 0.007 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00243 (12006) covalent geometry : angle 0.51275 (16338) hydrogen bonds : bond 0.10652 ( 655) hydrogen bonds : angle 5.73282 ( 1890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.436 Fit side-chains REVERT: A 29 GLN cc_start: 0.8015 (tt0) cc_final: 0.7787 (tm-30) REVERT: B 35 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6798 (mm-30) REVERT: B 36 SER cc_start: 0.8595 (m) cc_final: 0.8174 (t) REVERT: B 57 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.6981 (mtm110) REVERT: B 106 LYS cc_start: 0.7792 (mppt) cc_final: 0.7558 (mptp) REVERT: B 107 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6955 (pt0) REVERT: B 144 LYS cc_start: 0.7081 (mttt) cc_final: 0.6830 (mtpt) REVERT: C 57 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7663 (mtt180) REVERT: C 107 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7282 (pt0) REVERT: D 1 MET cc_start: 0.7854 (mpp) cc_final: 0.7473 (mtm) REVERT: D 20 MET cc_start: 0.7318 (mtp) cc_final: 0.6916 (ppp) REVERT: D 25 LYS cc_start: 0.7862 (ptmt) cc_final: 0.7643 (ptmm) REVERT: D 96 THR cc_start: 0.7931 (p) cc_final: 0.7618 (p) REVERT: D 146 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7935 (mt-10) REVERT: E 25 LYS cc_start: 0.7982 (pptt) cc_final: 0.7465 (pmtt) REVERT: E 107 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6635 (pt0) REVERT: F 1 MET cc_start: 0.7886 (mpp) cc_final: 0.7575 (mmm) REVERT: F 107 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6684 (pt0) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.6269 time to fit residues: 141.1622 Evaluate side-chains 141 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 overall best weight: 2.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN B 23 HIS B 29 GLN C 72 HIS E 87 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.186407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.150681 restraints weight = 12235.655| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.07 r_work: 0.3627 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12006 Z= 0.212 Angle : 0.587 7.422 16338 Z= 0.314 Chirality : 0.049 0.153 1980 Planarity : 0.005 0.042 2118 Dihedral : 4.434 16.301 1686 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.30 % Allowed : 12.11 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.20), residues: 1554 helix: 1.51 (0.20), residues: 582 sheet: 0.64 (0.28), residues: 330 loop : -1.07 (0.21), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 57 TYR 0.014 0.002 TYR E 120 PHE 0.015 0.002 PHE D 198 TRP 0.008 0.002 TRP C 30 HIS 0.010 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00498 (12006) covalent geometry : angle 0.58719 (16338) hydrogen bonds : bond 0.04343 ( 655) hydrogen bonds : angle 5.23772 ( 1890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 0.413 Fit side-chains REVERT: A 29 GLN cc_start: 0.8211 (tt0) cc_final: 0.7941 (tm-30) REVERT: B 36 SER cc_start: 0.8784 (m) cc_final: 0.8476 (t) REVERT: B 144 LYS cc_start: 0.7695 (mttt) cc_final: 0.7182 (mmpt) REVERT: C 29 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7485 (tt0) REVERT: C 107 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7432 (pt0) REVERT: D 1 MET cc_start: 0.8254 (mpp) cc_final: 0.7931 (mtm) REVERT: D 20 MET cc_start: 0.7700 (mtp) cc_final: 0.6894 (ppp) REVERT: D 25 LYS cc_start: 0.8024 (ptmt) cc_final: 0.7725 (ptpt) REVERT: D 46 THR cc_start: 0.8091 (t) cc_final: 0.7811 (m) REVERT: E 20 MET cc_start: 0.5330 (pmm) cc_final: 0.5065 (pmm) REVERT: E 72 HIS cc_start: 0.5580 (p-80) cc_final: 0.5335 (p-80) REVERT: E 107 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6591 (pt0) REVERT: E 235 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7284 (mt) REVERT: F 1 MET cc_start: 0.8087 (mpp) cc_final: 0.7603 (mmm) REVERT: F 20 MET cc_start: 0.6695 (pmm) cc_final: 0.5823 (ppp) REVERT: F 29 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: F 88 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8296 (m) REVERT: F 107 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6647 (pt0) REVERT: F 179 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7110 (ttp80) outliers start: 42 outliers final: 26 residues processed: 172 average time/residue: 0.5909 time to fit residues: 110.1887 Evaluate side-chains 169 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 179 ARG Chi-restraints excluded: chain F residue 222 VAL Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS E 87 HIS F 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.188150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152627 restraints weight = 12309.466| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.98 r_work: 0.3629 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12006 Z= 0.141 Angle : 0.502 6.137 16338 Z= 0.268 Chirality : 0.045 0.148 1980 Planarity : 0.004 0.040 2118 Dihedral : 4.171 16.245 1686 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.99 % Allowed : 13.99 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.20), residues: 1554 helix: 1.86 (0.21), residues: 582 sheet: 0.72 (0.28), residues: 330 loop : -0.94 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 57 TYR 0.012 0.001 TYR E 120 PHE 0.011 0.001 PHE A 198 TRP 0.009 0.001 TRP C 30 HIS 0.013 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00323 (12006) covalent geometry : angle 0.50168 (16338) hydrogen bonds : bond 0.03713 ( 655) hydrogen bonds : angle 4.99685 ( 1890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 0.420 Fit side-chains REVERT: A 29 GLN cc_start: 0.8200 (tt0) cc_final: 0.7915 (tm-30) REVERT: A 235 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7410 (mp) REVERT: A 260 ASN cc_start: 0.7563 (m-40) cc_final: 0.6934 (t0) REVERT: B 29 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: B 36 SER cc_start: 0.8770 (m) cc_final: 0.8454 (t) REVERT: B 144 LYS cc_start: 0.7649 (mttt) cc_final: 0.7152 (mmpt) REVERT: B 212 ASP cc_start: 0.7937 (m-30) cc_final: 0.7721 (m-30) REVERT: B 259 ARG cc_start: 0.7789 (ttm170) cc_final: 0.7588 (ttm170) REVERT: C 29 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: C 57 ARG cc_start: 0.8075 (mtm-85) cc_final: 0.7663 (mtt180) REVERT: C 107 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7376 (pt0) REVERT: D 1 MET cc_start: 0.8314 (mpp) cc_final: 0.7887 (mtm) REVERT: D 20 MET cc_start: 0.7675 (mtp) cc_final: 0.6800 (ppp) REVERT: D 25 LYS cc_start: 0.7969 (ptmt) cc_final: 0.7599 (ptmm) REVERT: D 46 THR cc_start: 0.8057 (t) cc_final: 0.7780 (m) REVERT: D 146 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8311 (mt-10) REVERT: E 20 MET cc_start: 0.5357 (pmm) cc_final: 0.5118 (pmm) REVERT: E 72 HIS cc_start: 0.5528 (p-80) cc_final: 0.5292 (p-80) REVERT: E 235 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7295 (mt) REVERT: F 1 MET cc_start: 0.8081 (mpp) cc_final: 0.7588 (mmm) REVERT: F 29 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: F 88 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8274 (m) REVERT: F 107 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6651 (pt0) outliers start: 38 outliers final: 26 residues processed: 163 average time/residue: 0.5776 time to fit residues: 102.1448 Evaluate side-chains 164 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 77 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN E 9 ASN E 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.189958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.154666 restraints weight = 12364.135| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.00 r_work: 0.3648 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12006 Z= 0.112 Angle : 0.466 7.097 16338 Z= 0.248 Chirality : 0.044 0.145 1980 Planarity : 0.004 0.040 2118 Dihedral : 3.923 16.042 1686 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.91 % Allowed : 15.09 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.21), residues: 1554 helix: 2.16 (0.21), residues: 582 sheet: 0.87 (0.29), residues: 312 loop : -0.67 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 57 TYR 0.009 0.001 TYR E 120 PHE 0.009 0.001 PHE A 198 TRP 0.008 0.001 TRP C 30 HIS 0.011 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00253 (12006) covalent geometry : angle 0.46642 (16338) hydrogen bonds : bond 0.03365 ( 655) hydrogen bonds : angle 4.81159 ( 1890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.442 Fit side-chains REVERT: A 29 GLN cc_start: 0.8177 (tt0) cc_final: 0.7909 (tm-30) REVERT: A 72 HIS cc_start: 0.6066 (OUTLIER) cc_final: 0.5240 (p-80) REVERT: A 235 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7375 (mp) REVERT: A 260 ASN cc_start: 0.7536 (m-40) cc_final: 0.6997 (t0) REVERT: B 29 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7752 (tm-30) REVERT: B 36 SER cc_start: 0.8752 (m) cc_final: 0.8414 (t) REVERT: B 144 LYS cc_start: 0.7642 (mttt) cc_final: 0.7139 (mmpt) REVERT: C 29 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: C 57 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7594 (mtt-85) REVERT: C 107 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7323 (pt0) REVERT: D 1 MET cc_start: 0.8294 (mpp) cc_final: 0.7940 (mtm) REVERT: D 20 MET cc_start: 0.7707 (mtp) cc_final: 0.6684 (ppp) REVERT: D 25 LYS cc_start: 0.7956 (ptmt) cc_final: 0.7606 (ptmm) REVERT: D 46 THR cc_start: 0.8033 (t) cc_final: 0.7751 (m) REVERT: D 146 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8323 (mt-10) REVERT: E 20 MET cc_start: 0.5270 (pmm) cc_final: 0.5029 (pmm) REVERT: E 72 HIS cc_start: 0.5483 (p-80) cc_final: 0.5249 (p-80) REVERT: E 235 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7275 (mt) REVERT: F 1 MET cc_start: 0.8059 (mpp) cc_final: 0.7556 (mmm) REVERT: F 20 MET cc_start: 0.6615 (pmm) cc_final: 0.5696 (ppp) REVERT: F 88 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8241 (m) REVERT: F 95 ARG cc_start: 0.6512 (mmm160) cc_final: 0.5833 (mtm-85) REVERT: F 107 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6714 (pt0) outliers start: 37 outliers final: 24 residues processed: 157 average time/residue: 0.6089 time to fit residues: 103.7210 Evaluate side-chains 162 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 92 optimal weight: 0.0770 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 113 optimal weight: 0.0010 chunk 101 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.191116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.155870 restraints weight = 12240.982| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.99 r_work: 0.3670 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12006 Z= 0.100 Angle : 0.446 5.182 16338 Z= 0.237 Chirality : 0.044 0.142 1980 Planarity : 0.004 0.040 2118 Dihedral : 3.762 15.622 1686 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.14 % Allowed : 15.96 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.21), residues: 1554 helix: 2.35 (0.21), residues: 582 sheet: 1.15 (0.29), residues: 300 loop : -0.58 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 57 TYR 0.008 0.001 TYR B 81 PHE 0.009 0.001 PHE A 198 TRP 0.007 0.001 TRP C 30 HIS 0.009 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00223 (12006) covalent geometry : angle 0.44552 (16338) hydrogen bonds : bond 0.03179 ( 655) hydrogen bonds : angle 4.70153 ( 1890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.515 Fit side-chains REVERT: A 29 GLN cc_start: 0.8157 (tt0) cc_final: 0.7913 (tm-30) REVERT: A 260 ASN cc_start: 0.7494 (m-40) cc_final: 0.7027 (t0) REVERT: B 29 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: B 36 SER cc_start: 0.8748 (m) cc_final: 0.8399 (t) REVERT: B 144 LYS cc_start: 0.7574 (mttt) cc_final: 0.7079 (mmpt) REVERT: B 259 ARG cc_start: 0.7705 (ttm170) cc_final: 0.7475 (ttm170) REVERT: C 29 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: C 107 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7278 (pt0) REVERT: D 1 MET cc_start: 0.8270 (mpp) cc_final: 0.7952 (mtm) REVERT: D 20 MET cc_start: 0.7643 (mtp) cc_final: 0.6725 (ppp) REVERT: D 25 LYS cc_start: 0.7935 (ptmt) cc_final: 0.7586 (ptmm) REVERT: D 46 THR cc_start: 0.7990 (t) cc_final: 0.7749 (m) REVERT: E 72 HIS cc_start: 0.5500 (OUTLIER) cc_final: 0.5202 (p-80) REVERT: E 235 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7240 (mt) REVERT: F 1 MET cc_start: 0.8007 (mpp) cc_final: 0.7496 (mmm) REVERT: F 20 MET cc_start: 0.6562 (pmm) cc_final: 0.5650 (ppp) REVERT: F 88 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8229 (m) REVERT: F 95 ARG cc_start: 0.6462 (mmm160) cc_final: 0.5816 (mtm-85) REVERT: F 107 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6720 (pt0) outliers start: 40 outliers final: 24 residues processed: 165 average time/residue: 0.6436 time to fit residues: 114.6902 Evaluate side-chains 157 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 87 HIS A 185 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.188842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.153137 restraints weight = 12223.767| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.99 r_work: 0.3647 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12006 Z= 0.127 Angle : 0.473 5.789 16338 Z= 0.252 Chirality : 0.045 0.143 1980 Planarity : 0.004 0.041 2118 Dihedral : 3.890 15.576 1686 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.62 % Allowed : 16.35 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.21), residues: 1554 helix: 2.25 (0.21), residues: 582 sheet: 0.97 (0.28), residues: 312 loop : -0.56 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 57 TYR 0.010 0.001 TYR E 120 PHE 0.011 0.001 PHE A 198 TRP 0.006 0.001 TRP C 30 HIS 0.006 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00288 (12006) covalent geometry : angle 0.47271 (16338) hydrogen bonds : bond 0.03444 ( 655) hydrogen bonds : angle 4.78944 ( 1890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 0.448 Fit side-chains REVERT: A 29 GLN cc_start: 0.8169 (tt0) cc_final: 0.7903 (tm-30) REVERT: A 260 ASN cc_start: 0.7527 (m-40) cc_final: 0.7010 (t0) REVERT: B 29 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7782 (tm-30) REVERT: B 36 SER cc_start: 0.8737 (m) cc_final: 0.8397 (t) REVERT: B 144 LYS cc_start: 0.7577 (mttt) cc_final: 0.7094 (mmpt) REVERT: C 29 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: C 57 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7643 (mtt-85) REVERT: C 107 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7311 (pt0) REVERT: D 1 MET cc_start: 0.8266 (mpp) cc_final: 0.7940 (mtm) REVERT: D 20 MET cc_start: 0.7647 (mtp) cc_final: 0.6755 (ppp) REVERT: D 25 LYS cc_start: 0.7982 (ptmt) cc_final: 0.7588 (ptmm) REVERT: D 46 THR cc_start: 0.8019 (t) cc_final: 0.7770 (m) REVERT: E 72 HIS cc_start: 0.5505 (OUTLIER) cc_final: 0.5237 (p-80) REVERT: E 235 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7251 (mt) REVERT: F 1 MET cc_start: 0.8003 (mpp) cc_final: 0.7489 (mmm) REVERT: F 29 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: F 88 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8229 (m) REVERT: F 95 ARG cc_start: 0.6505 (mmm160) cc_final: 0.5825 (mtm-85) REVERT: F 107 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6740 (pt0) outliers start: 46 outliers final: 32 residues processed: 160 average time/residue: 0.6269 time to fit residues: 108.6294 Evaluate side-chains 164 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN D 29 GLN E 9 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.184237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.147505 restraints weight = 12298.339| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.09 r_work: 0.3592 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12006 Z= 0.256 Angle : 0.607 7.859 16338 Z= 0.325 Chirality : 0.050 0.146 1980 Planarity : 0.005 0.049 2118 Dihedral : 4.504 16.409 1686 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 4.01 % Allowed : 16.59 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.20), residues: 1554 helix: 1.59 (0.20), residues: 582 sheet: 0.82 (0.28), residues: 312 loop : -0.76 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 57 TYR 0.019 0.002 TYR C 81 PHE 0.016 0.002 PHE D 198 TRP 0.008 0.002 TRP C 30 HIS 0.008 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00608 (12006) covalent geometry : angle 0.60748 (16338) hydrogen bonds : bond 0.04455 ( 655) hydrogen bonds : angle 5.22007 ( 1890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 135 time to evaluate : 0.482 Fit side-chains REVERT: A 29 GLN cc_start: 0.8239 (tt0) cc_final: 0.7953 (tm-30) REVERT: A 260 ASN cc_start: 0.7597 (m-40) cc_final: 0.6945 (t0) REVERT: B 36 SER cc_start: 0.8791 (m) cc_final: 0.8479 (t) REVERT: B 144 LYS cc_start: 0.7623 (mttt) cc_final: 0.7146 (mmpt) REVERT: B 166 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.5564 (ttp-110) REVERT: C 29 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: C 57 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7598 (mtt-85) REVERT: C 104 ASN cc_start: 0.7911 (m110) cc_final: 0.7568 (m-40) REVERT: C 107 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7385 (pt0) REVERT: D 1 MET cc_start: 0.8345 (mpp) cc_final: 0.7882 (mtm) REVERT: D 20 MET cc_start: 0.7731 (mtp) cc_final: 0.6737 (ppp) REVERT: D 25 LYS cc_start: 0.8033 (ptmt) cc_final: 0.7706 (ptpt) REVERT: D 46 THR cc_start: 0.8157 (t) cc_final: 0.7848 (m) REVERT: E 72 HIS cc_start: 0.5680 (OUTLIER) cc_final: 0.5416 (p-80) REVERT: E 235 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7298 (mt) REVERT: F 1 MET cc_start: 0.8103 (mpp) cc_final: 0.7595 (mmp) REVERT: F 20 MET cc_start: 0.6633 (pmm) cc_final: 0.5582 (ppp) REVERT: F 29 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: F 95 ARG cc_start: 0.6402 (mmm160) cc_final: 0.5666 (mtm-85) REVERT: F 107 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6745 (pt0) outliers start: 51 outliers final: 36 residues processed: 170 average time/residue: 0.5721 time to fit residues: 105.4115 Evaluate side-chains 174 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 112 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 10 optimal weight: 0.0000 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN E 9 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.187161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.151779 restraints weight = 12276.849| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.06 r_work: 0.3643 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12006 Z= 0.143 Angle : 0.508 6.573 16338 Z= 0.272 Chirality : 0.045 0.160 1980 Planarity : 0.004 0.043 2118 Dihedral : 4.209 16.344 1686 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.38 % Allowed : 17.45 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.20), residues: 1554 helix: 1.90 (0.21), residues: 582 sheet: 0.84 (0.28), residues: 312 loop : -0.64 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 57 TYR 0.013 0.002 TYR E 120 PHE 0.013 0.001 PHE F 196 TRP 0.008 0.001 TRP C 30 HIS 0.006 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00327 (12006) covalent geometry : angle 0.50766 (16338) hydrogen bonds : bond 0.03728 ( 655) hydrogen bonds : angle 4.97227 ( 1890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.393 Fit side-chains REVERT: A 29 GLN cc_start: 0.8179 (tt0) cc_final: 0.7885 (tm-30) REVERT: A 260 ASN cc_start: 0.7539 (m-40) cc_final: 0.6955 (t0) REVERT: B 36 SER cc_start: 0.8743 (m) cc_final: 0.8429 (t) REVERT: B 144 LYS cc_start: 0.7611 (mttt) cc_final: 0.7158 (mmpt) REVERT: B 166 ARG cc_start: 0.6292 (OUTLIER) cc_final: 0.5591 (ttp-110) REVERT: C 29 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: C 57 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7619 (mtt-85) REVERT: C 104 ASN cc_start: 0.7812 (m110) cc_final: 0.7484 (m-40) REVERT: C 107 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7369 (pt0) REVERT: D 1 MET cc_start: 0.8323 (mpp) cc_final: 0.7880 (mtm) REVERT: D 20 MET cc_start: 0.7718 (mtp) cc_final: 0.6783 (ppp) REVERT: D 25 LYS cc_start: 0.7996 (ptmt) cc_final: 0.7701 (ptpt) REVERT: D 46 THR cc_start: 0.8093 (t) cc_final: 0.7819 (m) REVERT: E 72 HIS cc_start: 0.5592 (OUTLIER) cc_final: 0.5343 (p-80) REVERT: E 235 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7253 (mt) REVERT: F 1 MET cc_start: 0.8045 (mpp) cc_final: 0.7542 (mmp) REVERT: F 20 MET cc_start: 0.6599 (pmm) cc_final: 0.5588 (ppp) REVERT: F 29 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: F 88 VAL cc_start: 0.8494 (p) cc_final: 0.8280 (m) REVERT: F 95 ARG cc_start: 0.6403 (mmm160) cc_final: 0.5670 (mtm-85) REVERT: F 107 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6685 (pt0) outliers start: 43 outliers final: 33 residues processed: 164 average time/residue: 0.5928 time to fit residues: 105.1371 Evaluate side-chains 173 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 84 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 54 optimal weight: 0.0050 chunk 15 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN D 29 GLN E 9 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.187151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.151474 restraints weight = 12188.730| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.07 r_work: 0.3635 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12006 Z= 0.162 Angle : 0.518 6.384 16338 Z= 0.277 Chirality : 0.046 0.152 1980 Planarity : 0.004 0.043 2118 Dihedral : 4.205 16.324 1686 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.54 % Allowed : 17.69 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.20), residues: 1554 helix: 1.89 (0.21), residues: 582 sheet: 0.82 (0.28), residues: 312 loop : -0.62 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 57 TYR 0.013 0.002 TYR E 120 PHE 0.013 0.002 PHE F 196 TRP 0.007 0.001 TRP C 30 HIS 0.005 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00377 (12006) covalent geometry : angle 0.51755 (16338) hydrogen bonds : bond 0.03805 ( 655) hydrogen bonds : angle 4.97729 ( 1890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 135 time to evaluate : 0.472 Fit side-chains REVERT: A 29 GLN cc_start: 0.8178 (tt0) cc_final: 0.7909 (tm-30) REVERT: A 260 ASN cc_start: 0.7574 (m-40) cc_final: 0.6929 (t0) REVERT: B 36 SER cc_start: 0.8755 (m) cc_final: 0.8433 (t) REVERT: B 144 LYS cc_start: 0.7595 (mttt) cc_final: 0.7140 (mmpt) REVERT: B 166 ARG cc_start: 0.6297 (OUTLIER) cc_final: 0.5596 (ttp-110) REVERT: B 259 ARG cc_start: 0.7630 (ttm170) cc_final: 0.7409 (mtm180) REVERT: C 29 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: C 57 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7614 (mtt-85) REVERT: C 104 ASN cc_start: 0.7825 (m110) cc_final: 0.7495 (m-40) REVERT: C 107 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7373 (pt0) REVERT: D 1 MET cc_start: 0.8331 (mpp) cc_final: 0.7870 (mtm) REVERT: D 20 MET cc_start: 0.7725 (mtp) cc_final: 0.6773 (ppp) REVERT: D 25 LYS cc_start: 0.8024 (ptmt) cc_final: 0.7709 (ptpt) REVERT: D 46 THR cc_start: 0.8102 (t) cc_final: 0.7819 (m) REVERT: E 72 HIS cc_start: 0.5599 (OUTLIER) cc_final: 0.5347 (p-80) REVERT: E 235 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7242 (mt) REVERT: F 1 MET cc_start: 0.8050 (mpp) cc_final: 0.7547 (mmp) REVERT: F 20 MET cc_start: 0.6603 (pmm) cc_final: 0.5586 (ppp) REVERT: F 29 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: F 88 VAL cc_start: 0.8465 (p) cc_final: 0.8244 (m) REVERT: F 95 ARG cc_start: 0.6423 (mmm160) cc_final: 0.5675 (mtm-85) REVERT: F 107 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6683 (pt0) outliers start: 45 outliers final: 34 residues processed: 167 average time/residue: 0.6232 time to fit residues: 112.9355 Evaluate side-chains 174 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN B 104 ASN E 9 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.189588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.154417 restraints weight = 12286.868| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.09 r_work: 0.3659 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12006 Z= 0.106 Angle : 0.467 6.202 16338 Z= 0.249 Chirality : 0.044 0.145 1980 Planarity : 0.004 0.042 2118 Dihedral : 3.948 16.151 1686 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.75 % Allowed : 18.55 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.21), residues: 1554 helix: 2.20 (0.21), residues: 582 sheet: 0.86 (0.29), residues: 312 loop : -0.49 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 57 TYR 0.010 0.001 TYR E 120 PHE 0.012 0.001 PHE F 196 TRP 0.011 0.001 TRP C 30 HIS 0.006 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00235 (12006) covalent geometry : angle 0.46733 (16338) hydrogen bonds : bond 0.03326 ( 655) hydrogen bonds : angle 4.79668 ( 1890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.487 Fit side-chains REVERT: A 29 GLN cc_start: 0.8162 (tt0) cc_final: 0.7880 (tm-30) REVERT: A 260 ASN cc_start: 0.7516 (m-40) cc_final: 0.6961 (t0) REVERT: B 36 SER cc_start: 0.8706 (m) cc_final: 0.8382 (t) REVERT: B 144 LYS cc_start: 0.7583 (mttt) cc_final: 0.7112 (mmpt) REVERT: B 259 ARG cc_start: 0.7595 (ttm170) cc_final: 0.7385 (mtm180) REVERT: C 29 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: C 107 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7396 (pt0) REVERT: D 1 MET cc_start: 0.8338 (mpp) cc_final: 0.7968 (mtm) REVERT: D 20 MET cc_start: 0.7715 (mtp) cc_final: 0.6771 (ppp) REVERT: D 25 LYS cc_start: 0.7972 (ptmt) cc_final: 0.7600 (ptmm) REVERT: D 46 THR cc_start: 0.8029 (t) cc_final: 0.7762 (m) REVERT: E 72 HIS cc_start: 0.5493 (OUTLIER) cc_final: 0.5223 (p-80) REVERT: E 91 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6023 (mm-30) REVERT: E 235 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7220 (mt) REVERT: F 1 MET cc_start: 0.8055 (mpp) cc_final: 0.7557 (mmp) REVERT: F 20 MET cc_start: 0.6471 (pmm) cc_final: 0.5492 (ppp) REVERT: F 29 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: F 88 VAL cc_start: 0.8438 (p) cc_final: 0.8219 (m) REVERT: F 95 ARG cc_start: 0.6366 (mmm160) cc_final: 0.5637 (mtm-85) REVERT: F 107 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6658 (pt0) outliers start: 35 outliers final: 27 residues processed: 160 average time/residue: 0.6485 time to fit residues: 112.2372 Evaluate side-chains 163 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.187532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151745 restraints weight = 12315.063| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.11 r_work: 0.3636 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12006 Z= 0.147 Angle : 0.504 6.294 16338 Z= 0.268 Chirality : 0.045 0.145 1980 Planarity : 0.004 0.043 2118 Dihedral : 4.068 16.260 1686 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.30 % Allowed : 18.08 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.21), residues: 1554 helix: 2.12 (0.21), residues: 582 sheet: 0.89 (0.28), residues: 312 loop : -0.52 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 57 TYR 0.011 0.002 TYR E 120 PHE 0.012 0.001 PHE C 198 TRP 0.006 0.001 TRP C 30 HIS 0.006 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00340 (12006) covalent geometry : angle 0.50370 (16338) hydrogen bonds : bond 0.03640 ( 655) hydrogen bonds : angle 4.89016 ( 1890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4573.30 seconds wall clock time: 78 minutes 35.56 seconds (4715.56 seconds total)