Starting phenix.real_space_refine on Sat Jan 18 01:22:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b78_44303/01_2025/9b78_44303.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b78_44303/01_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_44303/01_2025/9b78_44303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b78_44303/01_2025/9b78_44303.map" model { file = "/net/cci-nas-00/data/ceres_data/9b78_44303/01_2025/9b78_44303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b78_44303/01_2025/9b78_44303.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.055 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-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 6.90, per 1000 atoms: 0.58 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: 2.70 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.48 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: 3.63 Time building geometry restraints manager: 3.15 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: 0.02 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: 0.970 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 27.970 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.750 ------------------------------------------------------------------------------- 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= 0.163 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (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 TRP 0.014 0.002 TRP C 30 HIS 0.007 0.001 HIS C 72 PHE 0.006 0.001 PHE F 198 TYR 0.006 0.001 TYR E 120 ARG 0.005 0.001 ARG A 75 *********************** 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 : 1.419 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: 1.3750 time to fit residues: 310.4049 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 : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 63 optimal weight: 0.5980 chunk 122 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN B 29 GLN C 72 HIS E 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.184058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.147992 restraints weight = 12239.701| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.97 r_work: 0.3584 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 12006 Z= 0.520 Angle : 0.696 8.056 16338 Z= 0.372 Chirality : 0.053 0.170 1980 Planarity : 0.006 0.059 2118 Dihedral : 4.795 16.969 1686 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.46 % Allowed : 12.50 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.20), residues: 1554 helix: 0.97 (0.20), residues: 582 sheet: 0.57 (0.28), residues: 330 loop : -1.21 (0.21), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP F 30 HIS 0.011 0.002 HIS E 87 PHE 0.019 0.002 PHE D 198 TYR 0.019 0.003 TYR C 81 ARG 0.005 0.001 ARG C 8 *********************** 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 187 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8240 (tt0) cc_final: 0.7919 (tm-30) REVERT: B 36 SER cc_start: 0.8813 (m) cc_final: 0.8507 (t) REVERT: B 144 LYS cc_start: 0.7641 (mttt) cc_final: 0.7170 (mmpt) REVERT: C 29 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: C 107 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7424 (pt0) REVERT: C 146 GLU cc_start: 0.7742 (mp0) cc_final: 0.7332 (mp0) REVERT: C 237 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.7912 (mm-30) REVERT: D 1 MET cc_start: 0.8290 (mpp) cc_final: 0.7795 (mtm) REVERT: D 20 MET cc_start: 0.7748 (mtp) cc_final: 0.6925 (ppp) REVERT: D 25 LYS cc_start: 0.8036 (ptmt) cc_final: 0.7724 (ptpt) REVERT: D 46 THR cc_start: 0.8214 (t) cc_final: 0.7859 (m) REVERT: D 146 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8342 (mt-10) REVERT: E 224 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8080 (mm) REVERT: E 235 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7341 (mt) REVERT: F 1 MET cc_start: 0.8149 (mpp) cc_final: 0.7638 (mmm) REVERT: F 29 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: F 88 VAL cc_start: 0.8579 (p) cc_final: 0.8343 (m) REVERT: F 107 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6701 (pt0) outliers start: 44 outliers final: 30 residues processed: 171 average time/residue: 1.2944 time to fit residues: 239.7198 Evaluate side-chains 172 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 1.700 ------------------------------------------------------------------------------- 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 235 LEU 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 134 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 237 GLU 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 46 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 85 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 49 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 76 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN E 87 HIS E 191 GLN F 185 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.189469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153784 restraints weight = 12273.585| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.99 r_work: 0.3654 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1486 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= 0.160 Angle : 0.478 5.940 16338 Z= 0.256 Chirality : 0.044 0.148 1980 Planarity : 0.004 0.040 2118 Dihedral : 4.111 16.672 1686 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.99 % Allowed : 14.70 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.20), residues: 1554 helix: 1.88 (0.21), residues: 582 sheet: 0.87 (0.29), residues: 318 loop : -0.95 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 30 HIS 0.011 0.001 HIS E 87 PHE 0.009 0.001 PHE A 198 TYR 0.011 0.001 TYR E 120 ARG 0.005 0.000 ARG A 57 *********************** 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 180 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 1.442 Fit side-chains REVERT: A 29 GLN cc_start: 0.8195 (tt0) cc_final: 0.7918 (tm-30) REVERT: A 260 ASN cc_start: 0.7472 (m-40) cc_final: 0.6934 (t0) REVERT: B 36 SER cc_start: 0.8745 (m) cc_final: 0.8427 (t) REVERT: B 144 LYS cc_start: 0.7649 (mttt) cc_final: 0.7139 (mmpt) REVERT: B 212 ASP cc_start: 0.7906 (m-30) cc_final: 0.7701 (m-30) REVERT: C 29 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: C 57 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7478 (mtt-85) REVERT: C 107 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7341 (pt0) REVERT: D 1 MET cc_start: 0.8281 (mpp) cc_final: 0.7941 (mtm) REVERT: D 20 MET cc_start: 0.7700 (mtp) cc_final: 0.6750 (ppp) REVERT: D 25 LYS cc_start: 0.7976 (ptmt) cc_final: 0.7601 (ptmm) REVERT: D 46 THR cc_start: 0.8034 (t) cc_final: 0.7780 (m) REVERT: D 96 THR cc_start: 0.8254 (p) cc_final: 0.8006 (p) REVERT: D 146 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8461 (mt-10) REVERT: E 235 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7271 (mt) REVERT: F 1 MET cc_start: 0.8116 (mpp) cc_final: 0.7672 (mmm) REVERT: F 20 MET cc_start: 0.6673 (pmm) cc_final: 0.5759 (ppp) REVERT: F 88 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8252 (m) REVERT: F 107 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6711 (pt0) outliers start: 38 outliers final: 19 residues processed: 165 average time/residue: 1.2841 time to fit residues: 230.3039 Evaluate side-chains 157 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 235 LEU 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 230 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 62 optimal weight: 8.9990 chunk 106 optimal weight: 0.2980 chunk 129 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.187209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.151087 restraints weight = 12237.752| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.06 r_work: 0.3622 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12006 Z= 0.246 Angle : 0.511 6.416 16338 Z= 0.274 Chirality : 0.046 0.146 1980 Planarity : 0.004 0.042 2118 Dihedral : 4.186 16.737 1686 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.54 % Allowed : 14.86 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.21), residues: 1554 helix: 1.90 (0.21), residues: 582 sheet: 0.80 (0.29), residues: 312 loop : -0.79 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 30 HIS 0.014 0.001 HIS E 72 PHE 0.013 0.002 PHE A 198 TYR 0.012 0.002 TYR E 120 ARG 0.005 0.000 ARG A 57 *********************** 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 179 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 134 time to evaluate : 1.336 Fit side-chains REVERT: A 29 GLN cc_start: 0.8182 (tt0) cc_final: 0.7895 (tm-30) REVERT: A 235 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7417 (mp) REVERT: A 260 ASN cc_start: 0.7494 (m-40) cc_final: 0.6911 (t0) REVERT: B 29 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: B 36 SER cc_start: 0.8786 (m) cc_final: 0.8468 (t) REVERT: B 144 LYS cc_start: 0.7650 (mttt) cc_final: 0.7153 (mmpt) REVERT: C 29 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: C 57 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7514 (mtt-85) REVERT: C 107 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7368 (pt0) REVERT: D 1 MET cc_start: 0.8292 (mpp) cc_final: 0.7821 (mtm) REVERT: D 20 MET cc_start: 0.7718 (mtp) cc_final: 0.6665 (ppp) REVERT: D 25 LYS cc_start: 0.7982 (ptmt) cc_final: 0.7608 (ptmm) REVERT: D 46 THR cc_start: 0.8096 (t) cc_final: 0.7809 (m) REVERT: D 96 THR cc_start: 0.8318 (p) cc_final: 0.8098 (p) REVERT: E 72 HIS cc_start: 0.5743 (OUTLIER) cc_final: 0.4989 (p-80) REVERT: E 235 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7298 (mt) REVERT: F 1 MET cc_start: 0.8099 (mpp) cc_final: 0.7606 (mmp) REVERT: F 88 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8283 (m) REVERT: F 107 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6737 (pt0) outliers start: 45 outliers final: 32 residues processed: 163 average time/residue: 1.2873 time to fit residues: 227.9143 Evaluate side-chains 168 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 224 ILE 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 235 LEU Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 173 VAL 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 46 THR 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 235 LEU 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 88 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 214 SER 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 141 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 185 ASN E 9 ASN E 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.188604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.152875 restraints weight = 12171.593| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.11 r_work: 0.3644 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12006 Z= 0.200 Angle : 0.481 7.207 16338 Z= 0.257 Chirality : 0.045 0.144 1980 Planarity : 0.004 0.042 2118 Dihedral : 4.032 16.553 1686 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.77 % Allowed : 15.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.21), residues: 1554 helix: 2.07 (0.21), residues: 582 sheet: 0.85 (0.29), residues: 312 loop : -0.69 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 30 HIS 0.014 0.001 HIS E 72 PHE 0.011 0.001 PHE A 198 TYR 0.011 0.001 TYR E 120 ARG 0.005 0.000 ARG A 57 *********************** 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 181 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 1.299 Fit side-chains REVERT: A 29 GLN cc_start: 0.8178 (tt0) cc_final: 0.7893 (tm-30) REVERT: A 260 ASN cc_start: 0.7462 (m-40) cc_final: 0.6943 (t0) REVERT: B 29 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: B 36 SER cc_start: 0.8758 (m) cc_final: 0.8433 (t) REVERT: B 144 LYS cc_start: 0.7624 (mttt) cc_final: 0.7124 (mmpt) REVERT: B 166 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5894 (mtp85) REVERT: C 29 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7461 (tt0) REVERT: C 57 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7708 (mtt180) REVERT: C 107 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7384 (pt0) REVERT: D 1 MET cc_start: 0.8289 (mpp) cc_final: 0.7840 (mtm) REVERT: D 20 MET cc_start: 0.7715 (mtp) cc_final: 0.6762 (ppp) REVERT: D 25 LYS cc_start: 0.7978 (ptmt) cc_final: 0.7592 (ptmm) REVERT: D 46 THR cc_start: 0.8054 (t) cc_final: 0.7781 (m) REVERT: E 235 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7271 (mt) REVERT: F 1 MET cc_start: 0.8023 (mpp) cc_final: 0.7540 (mmp) REVERT: F 20 MET cc_start: 0.6665 (pmm) cc_final: 0.5777 (ppp) REVERT: F 88 VAL cc_start: 0.8460 (OUTLIER) cc_final: 0.8251 (m) REVERT: F 107 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6712 (pt0) outliers start: 48 outliers final: 33 residues processed: 166 average time/residue: 1.2777 time to fit residues: 230.4808 Evaluate side-chains 167 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 108 VAL Chi-restraints excluded: chain A residue 224 ILE 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 134 SER 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 173 VAL 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 156 VAL Chi-restraints excluded: chain E residue 235 LEU 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 173 VAL Chi-restraints excluded: chain F residue 214 SER 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 3 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 151 optimal weight: 0.0870 chunk 40 optimal weight: 0.5980 chunk 105 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 88 optimal weight: 0.0040 overall best weight: 1.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4138 r_free = 0.4138 target = 0.188841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153054 restraints weight = 12315.026| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.03 r_work: 0.3642 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1719 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= 0.199 Angle : 0.479 5.799 16338 Z= 0.256 Chirality : 0.045 0.145 1980 Planarity : 0.004 0.042 2118 Dihedral : 3.987 16.306 1686 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 4.01 % Allowed : 16.12 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.21), residues: 1554 helix: 2.11 (0.21), residues: 582 sheet: 0.88 (0.29), residues: 312 loop : -0.63 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 30 HIS 0.015 0.001 HIS E 72 PHE 0.011 0.001 PHE A 198 TYR 0.010 0.001 TYR E 120 ARG 0.006 0.000 ARG A 57 *********************** 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 178 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 1.309 Fit side-chains REVERT: A 29 GLN cc_start: 0.8185 (tt0) cc_final: 0.7923 (tm-30) REVERT: A 260 ASN cc_start: 0.7504 (m-40) cc_final: 0.6999 (t0) REVERT: B 29 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: B 36 SER cc_start: 0.8756 (m) cc_final: 0.8430 (t) REVERT: B 144 LYS cc_start: 0.7626 (mttt) cc_final: 0.7135 (mmpt) REVERT: B 166 ARG cc_start: 0.6318 (OUTLIER) cc_final: 0.5568 (ttp-110) REVERT: C 29 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7467 (tt0) REVERT: C 57 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7712 (mtt180) REVERT: C 107 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7409 (pt0) REVERT: D 1 MET cc_start: 0.8304 (mpp) cc_final: 0.7857 (mtm) REVERT: D 20 MET cc_start: 0.7720 (mtp) cc_final: 0.6770 (ppp) REVERT: D 25 LYS cc_start: 0.7995 (ptmt) cc_final: 0.7611 (ptmm) REVERT: D 46 THR cc_start: 0.8057 (t) cc_final: 0.7775 (m) REVERT: E 72 HIS cc_start: 0.5773 (OUTLIER) cc_final: 0.5171 (p-80) REVERT: E 235 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7245 (mt) REVERT: F 1 MET cc_start: 0.8042 (mpp) cc_final: 0.7540 (mmm) REVERT: F 20 MET cc_start: 0.6591 (pmm) cc_final: 0.5696 (ppp) REVERT: F 88 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8263 (m) REVERT: F 95 ARG cc_start: 0.6471 (mmm160) cc_final: 0.5679 (mtm-85) REVERT: F 107 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6707 (pt0) outliers start: 51 outliers final: 36 residues processed: 164 average time/residue: 1.2880 time to fit residues: 229.5358 Evaluate side-chains 169 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 108 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 134 SER 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 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 134 SER Chi-restraints excluded: chain D residue 173 VAL 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 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 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 110 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4084 r_free = 0.4084 target = 0.183494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.147435 restraints weight = 12372.813| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.11 r_work: 0.3592 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 12006 Z= 0.471 Angle : 0.633 7.293 16338 Z= 0.340 Chirality : 0.052 0.144 1980 Planarity : 0.005 0.051 2118 Dihedral : 4.621 17.064 1686 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 4.17 % Allowed : 17.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1554 helix: 1.36 (0.20), residues: 582 sheet: 0.72 (0.29), residues: 312 loop : -0.87 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP C 30 HIS 0.016 0.002 HIS E 72 PHE 0.017 0.002 PHE C 198 TYR 0.019 0.003 TYR E 120 ARG 0.006 0.001 ARG A 57 *********************** 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 183 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 130 time to evaluate : 1.250 Fit side-chains REVERT: A 29 GLN cc_start: 0.8267 (tt0) cc_final: 0.7979 (tm-30) REVERT: B 36 SER cc_start: 0.8787 (m) cc_final: 0.8489 (t) REVERT: B 144 LYS cc_start: 0.7621 (mttt) cc_final: 0.7157 (mmpt) REVERT: B 148 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8482 (mp) REVERT: B 166 ARG cc_start: 0.6331 (OUTLIER) cc_final: 0.5918 (mtp85) REVERT: C 29 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7478 (tt0) REVERT: C 57 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7715 (mtt180) REVERT: C 107 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7407 (pt0) REVERT: D 1 MET cc_start: 0.8328 (mpp) cc_final: 0.7969 (mtm) REVERT: D 20 MET cc_start: 0.7758 (mtp) cc_final: 0.6759 (ppp) REVERT: D 25 LYS cc_start: 0.8033 (ptmt) cc_final: 0.7757 (ptpt) REVERT: D 46 THR cc_start: 0.8193 (t) cc_final: 0.7841 (m) REVERT: E 72 HIS cc_start: 0.5889 (OUTLIER) cc_final: 0.5080 (p-80) REVERT: F 107 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6771 (pt0) outliers start: 53 outliers final: 38 residues processed: 170 average time/residue: 1.2342 time to fit residues: 228.6312 Evaluate side-chains 172 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 32 ILE 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 235 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 148 LEU 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 114 VAL Chi-restraints excluded: chain D residue 173 VAL 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 46 THR 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 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 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 119 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4133 r_free = 0.4133 target = 0.188542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.153116 restraints weight = 12307.894| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.08 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: 0.8043 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12006 Z= 0.164 Angle : 0.474 7.838 16338 Z= 0.253 Chirality : 0.044 0.144 1980 Planarity : 0.004 0.043 2118 Dihedral : 4.022 16.808 1686 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.83 % Allowed : 19.10 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.21), residues: 1554 helix: 2.04 (0.21), residues: 582 sheet: 0.84 (0.29), residues: 312 loop : -0.63 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 30 HIS 0.015 0.001 HIS E 72 PHE 0.010 0.001 PHE F 196 TYR 0.011 0.001 TYR B 81 ARG 0.007 0.000 ARG A 57 *********************** 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 172 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 1.481 Fit side-chains REVERT: A 29 GLN cc_start: 0.8185 (tt0) cc_final: 0.7895 (tm-30) REVERT: A 260 ASN cc_start: 0.7556 (m-40) cc_final: 0.6957 (t0) REVERT: B 36 SER cc_start: 0.8712 (m) cc_final: 0.8391 (t) REVERT: B 144 LYS cc_start: 0.7609 (mttt) cc_final: 0.7125 (mmpt) REVERT: B 166 ARG cc_start: 0.6275 (OUTLIER) cc_final: 0.5862 (mtp85) REVERT: B 259 ARG cc_start: 0.7606 (ttm170) cc_final: 0.7382 (mtm180) REVERT: C 29 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: C 57 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7647 (mtt180) REVERT: C 107 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7350 (pt0) REVERT: D 1 MET cc_start: 0.8341 (mpp) cc_final: 0.7888 (mtm) REVERT: D 20 MET cc_start: 0.7710 (mtp) cc_final: 0.6760 (ppp) REVERT: D 25 LYS cc_start: 0.7974 (ptmt) cc_final: 0.7591 (ptmm) REVERT: D 46 THR cc_start: 0.8043 (t) cc_final: 0.7800 (m) REVERT: E 235 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7212 (mt) REVERT: F 1 MET cc_start: 0.8225 (mtm) cc_final: 0.7510 (mmm) REVERT: F 20 MET cc_start: 0.6682 (pmm) cc_final: 0.5641 (ppp) REVERT: F 88 VAL cc_start: 0.8495 (p) cc_final: 0.8291 (m) REVERT: F 107 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6673 (pt0) outliers start: 36 outliers final: 25 residues processed: 162 average time/residue: 1.2926 time to fit residues: 229.0104 Evaluate side-chains 163 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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 235 LEU Chi-restraints excluded: chain B residue 27 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 88 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 61 THR 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 156 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 74 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 3 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 135 optimal weight: 0.0670 chunk 45 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.0040 chunk 127 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 overall best weight: 2.0134 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.186655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.150961 restraints weight = 12254.188| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.03 r_work: 0.3627 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12006 Z= 0.262 Angle : 0.522 7.022 16338 Z= 0.278 Chirality : 0.046 0.155 1980 Planarity : 0.004 0.045 2118 Dihedral : 4.176 16.781 1686 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.38 % Allowed : 18.55 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1554 helix: 1.94 (0.21), residues: 582 sheet: 0.82 (0.29), residues: 312 loop : -0.64 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 30 HIS 0.015 0.001 HIS E 72 PHE 0.013 0.002 PHE F 196 TYR 0.013 0.002 TYR E 120 ARG 0.007 0.000 ARG A 57 *********************** 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 174 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 1.742 Fit side-chains REVERT: A 29 GLN cc_start: 0.8186 (tt0) cc_final: 0.7905 (tm-30) REVERT: A 260 ASN cc_start: 0.7618 (m-40) cc_final: 0.6940 (t0) REVERT: B 36 SER cc_start: 0.8760 (m) cc_final: 0.8439 (t) REVERT: B 144 LYS cc_start: 0.7637 (mttt) cc_final: 0.7148 (mmpt) REVERT: B 166 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.5903 (mtp85) REVERT: B 259 ARG cc_start: 0.7653 (ttm170) cc_final: 0.7402 (mtm180) REVERT: C 29 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: C 57 ARG cc_start: 0.8122 (mtm-85) cc_final: 0.7705 (mtt180) REVERT: C 107 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7362 (pt0) REVERT: D 1 MET cc_start: 0.8323 (mpp) cc_final: 0.7851 (mtm) REVERT: D 20 MET cc_start: 0.7711 (mtp) cc_final: 0.6761 (ppp) REVERT: D 25 LYS cc_start: 0.8068 (ptmt) cc_final: 0.7652 (ptmm) REVERT: D 46 THR cc_start: 0.8099 (t) cc_final: 0.7814 (m) REVERT: E 235 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7239 (mt) REVERT: F 1 MET cc_start: 0.8270 (mtm) cc_final: 0.7526 (mmm) REVERT: F 20 MET cc_start: 0.6658 (pmm) cc_final: 0.5608 (ppp) REVERT: F 88 VAL cc_start: 0.8489 (p) cc_final: 0.8273 (m) REVERT: F 107 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6743 (pt0) outliers start: 43 outliers final: 31 residues processed: 162 average time/residue: 1.2837 time to fit residues: 226.2915 Evaluate side-chains 165 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 134 SER 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 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 114 VAL Chi-restraints excluded: chain D residue 230 THR 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 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 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 213 VAL 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 81 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 36 optimal weight: 0.0980 chunk 54 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.4138 r_free = 0.4138 target = 0.189090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.153251 restraints weight = 12187.263| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.04 r_work: 0.3654 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12006 Z= 0.171 Angle : 0.470 7.011 16338 Z= 0.250 Chirality : 0.044 0.147 1980 Planarity : 0.004 0.043 2118 Dihedral : 3.906 16.525 1686 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.75 % Allowed : 19.10 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.21), residues: 1554 helix: 2.21 (0.21), residues: 582 sheet: 0.85 (0.30), residues: 276 loop : -0.43 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 30 HIS 0.014 0.001 HIS E 72 PHE 0.011 0.001 PHE F 196 TYR 0.010 0.001 TYR B 81 ARG 0.007 0.000 ARG A 57 ********************** 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 166 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 1.380 Fit side-chains REVERT: A 29 GLN cc_start: 0.8185 (tt0) cc_final: 0.7901 (tm-30) REVERT: A 260 ASN cc_start: 0.7546 (m-40) cc_final: 0.6963 (t0) REVERT: B 36 SER cc_start: 0.8745 (m) cc_final: 0.8398 (t) REVERT: B 144 LYS cc_start: 0.7588 (mttt) cc_final: 0.7090 (mmpt) REVERT: B 166 ARG cc_start: 0.6274 (OUTLIER) cc_final: 0.5532 (ttp-110) REVERT: B 259 ARG cc_start: 0.7603 (ttm170) cc_final: 0.7388 (mtm180) REVERT: C 29 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: C 57 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7673 (mtt180) REVERT: C 107 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7389 (pt0) REVERT: D 1 MET cc_start: 0.8335 (mpp) cc_final: 0.7946 (mtm) REVERT: D 20 MET cc_start: 0.7696 (mtp) cc_final: 0.6742 (ppp) REVERT: D 25 LYS cc_start: 0.8022 (ptmt) cc_final: 0.7611 (ptmm) REVERT: D 46 THR cc_start: 0.8036 (t) cc_final: 0.7773 (m) REVERT: E 235 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7204 (mt) REVERT: F 1 MET cc_start: 0.8255 (mtm) cc_final: 0.7530 (mmm) REVERT: F 20 MET cc_start: 0.6534 (pmm) cc_final: 0.5539 (ppp) REVERT: F 46 THR cc_start: 0.8415 (t) cc_final: 0.8213 (p) REVERT: F 88 VAL cc_start: 0.8460 (p) cc_final: 0.8236 (m) REVERT: F 107 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6706 (pt0) outliers start: 35 outliers final: 29 residues processed: 159 average time/residue: 1.3057 time to fit residues: 225.2592 Evaluate side-chains 161 residues out of total 1272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 1.314 ------------------------------------------------------------------------------- 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 235 LEU Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 134 SER 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 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 114 VAL Chi-restraints excluded: chain D residue 230 THR 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 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 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 67 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.185484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.149212 restraints weight = 12241.148| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.15 r_work: 0.3612 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12006 Z= 0.327 Angle : 0.560 7.150 16338 Z= 0.298 Chirality : 0.048 0.153 1980 Planarity : 0.004 0.044 2118 Dihedral : 4.305 16.879 1686 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.22 % Allowed : 18.55 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1554 helix: 1.81 (0.21), residues: 582 sheet: 0.83 (0.28), residues: 312 loop : -0.63 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 30 HIS 0.015 0.001 HIS E 72 PHE 0.015 0.002 PHE F 196 TYR 0.015 0.002 TYR C 81 ARG 0.007 0.000 ARG A 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9137.65 seconds wall clock time: 163 minutes 34.84 seconds (9814.84 seconds total)