Starting phenix.real_space_refine on Fri Oct 23 06:48:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m7h_63683/10_2026/9m7h_63683.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m7h_63683/10_2026/9m7h_63683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m7h_63683/10_2026/9m7h_63683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m7h_63683/10_2026/9m7h_63683.map" model { file = "/net/cci-nas-00/data/ceres_data/9m7h_63683/10_2026/9m7h_63683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m7h_63683/10_2026/9m7h_63683.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.108 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3828 atoms to isotropic. 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 22 5.16 5 C 3687 2.51 5 N 939 2.21 5 O 1027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5675 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1993 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 6, 'TRANS': 245} Chain breaks: 4 Chain: "B" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 469 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "B" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1025 Unusual residues: {'CRO': 1} Classifications: {'peptide': 121, 'undetermined': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 117, None: 1} Not linked: pdbres="CRO B 68 " pdbres="VAL B 70 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'CRO:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2160 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 8, 'TRANS': 278} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.31, per 1000 atoms: 0.23 Number of scatterers: 5675 At special positions: 0 Unit cell: (67.1, 99, 121, 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 22 16.00 O 1027 8.00 N 939 7.00 C 3687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS C 186 " distance=2.05 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 303.5 milliseconds 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1336 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 56.8% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 23 through 49 removed outlier: 4.009A pdb=" N ARG A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 59 through 80 removed outlier: 3.525A pdb=" N GLN A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 120 removed outlier: 3.885A pdb=" N TYR A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 150 removed outlier: 4.682A pdb=" N CYS A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 190 removed outlier: 3.876A pdb=" N VAL A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 227 removed outlier: 4.307A pdb=" N ILE A 206 " --> pdb=" O HIS A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 257 removed outlier: 3.531A pdb=" N CYS A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 270 removed outlier: 3.597A pdb=" N CYS A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 10 removed outlier: 3.546A pdb=" N LEU B 9 " --> pdb=" O GLY B 6 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 10 " --> pdb=" O GLU B 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 6 through 10' Processing helix chain 'B' and resid 58 through 63 removed outlier: 3.629A pdb=" N VAL B 63 " --> pdb=" O PRO B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.835A pdb=" N PHE B 73 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER B 74 " --> pdb=" O GLN B 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 70 through 74' Processing helix chain 'B' and resid 77 through 84 removed outlier: 3.919A pdb=" N LYS B 81 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ARG B 82 " --> pdb=" O HIS B 79 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP B 84 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 14 through 24 Processing helix chain 'C' and resid 37 through 46 Processing helix chain 'C' and resid 47 through 58 Processing helix chain 'C' and resid 70 through 79 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 113 through 123 removed outlier: 3.503A pdb=" N TYR C 123 " --> pdb=" O VAL C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 144 removed outlier: 3.707A pdb=" N ASN C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 155 removed outlier: 4.056A pdb=" N LYS C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 181 removed outlier: 3.519A pdb=" N ALA C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 195 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 227 Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 250 through 260 Processing helix chain 'C' and resid 273 through 281 removed outlier: 3.610A pdb=" N ASN C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 294 removed outlier: 3.528A pdb=" N ALA C 287 " --> pdb=" O ASN C 283 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.679A pdb=" N ILE B 163 " --> pdb=" O ASN B 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 162 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 154 " --> pdb=" O HIS A1006 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS A1006 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A1027 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 46 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A1029 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 44 " --> pdb=" O GLU A1029 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N LEU B 121 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ASN B 123 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU B 17 " --> pdb=" O ASN B 123 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ILE B 125 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU B 19 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU B 127 " --> pdb=" O GLU B 19 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP B 21 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N GLY B 129 " --> pdb=" O ASP B 21 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP B 23 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B 120 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B 130 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 107 " --> pdb=" O ILE B 130 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 957 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: 0.79 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 957 1.30 - 1.42: 1435 1.42 - 1.55: 3366 1.55 - 1.68: 4 1.68 - 1.81: 30 Bond restraints: 5792 Sorted by residual: bond pdb=" CA ASP C 235 " pdb=" C ASP C 235 " ideal model delta sigma weight residual 1.528 1.422 0.106 1.28e-02 6.10e+03 6.91e+01 bond pdb=" C1 CRO B 68 " pdb=" N2 CRO B 68 " ideal model delta sigma weight residual 1.289 1.419 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" C VAL B 178 " pdb=" O VAL B 178 " ideal model delta sigma weight residual 1.236 1.179 0.057 9.90e-03 1.02e+04 3.30e+01 bond pdb=" C ASN B 172 " pdb=" O ASN B 172 " ideal model delta sigma weight residual 1.234 1.166 0.069 1.22e-02 6.72e+03 3.17e+01 bond pdb=" C2 CRO B 68 " pdb=" N3 CRO B 68 " ideal model delta sigma weight residual 1.375 1.483 -0.108 2.00e-02 2.50e+03 2.90e+01 ... (remaining 5787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 7724 3.27 - 6.55: 117 6.55 - 9.82: 26 9.82 - 13.09: 3 13.09 - 16.37: 1 Bond angle restraints: 7871 Sorted by residual: angle pdb=" N ASP C 234 " pdb=" CA ASP C 234 " pdb=" C ASP C 234 " ideal model delta sigma weight residual 108.90 121.72 -12.82 1.63e+00 3.76e-01 6.19e+01 angle pdb=" O VAL C 152 " pdb=" C VAL C 152 " pdb=" N LEU C 153 " ideal model delta sigma weight residual 121.83 114.18 7.65 1.03e+00 9.43e-01 5.52e+01 angle pdb=" N LEU C 153 " pdb=" CA LEU C 153 " pdb=" C LEU C 153 " ideal model delta sigma weight residual 111.82 120.10 -8.28 1.16e+00 7.43e-01 5.09e+01 angle pdb=" N GLU B 174 " pdb=" CA GLU B 174 " pdb=" C GLU B 174 " ideal model delta sigma weight residual 112.87 121.34 -8.47 1.20e+00 6.94e-01 4.98e+01 angle pdb=" CA VAL C 152 " pdb=" C VAL C 152 " pdb=" N LEU C 153 " ideal model delta sigma weight residual 117.28 124.93 -7.65 1.16e+00 7.43e-01 4.35e+01 ... (remaining 7866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 3101 17.24 - 34.47: 278 34.47 - 51.71: 46 51.71 - 68.95: 4 68.95 - 86.18: 5 Dihedral angle restraints: 3434 sinusoidal: 1366 harmonic: 2068 Sorted by residual: dihedral pdb=" N GLN C 236 " pdb=" C GLN C 236 " pdb=" CA GLN C 236 " pdb=" CB GLN C 236 " ideal model delta harmonic sigma weight residual 122.80 145.05 -22.25 0 2.50e+00 1.60e-01 7.92e+01 dihedral pdb=" C GLN C 236 " pdb=" N GLN C 236 " pdb=" CA GLN C 236 " pdb=" CB GLN C 236 " ideal model delta harmonic sigma weight residual -122.60 -144.78 22.18 0 2.50e+00 1.60e-01 7.87e+01 dihedral pdb=" CB CYS A 121 " pdb=" SG CYS A 121 " pdb=" SG CYS C 186 " pdb=" CB CYS C 186 " ideal model delta sinusoidal sigma weight residual 93.00 130.78 -37.78 1 1.00e+01 1.00e-02 2.01e+01 ... (remaining 3431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.217: 915 0.217 - 0.435: 7 0.435 - 0.652: 3 0.652 - 0.869: 0 0.869 - 1.087: 1 Chirality restraints: 926 Sorted by residual: chirality pdb=" CA GLN C 236 " pdb=" N GLN C 236 " pdb=" C GLN C 236 " pdb=" CB GLN C 236 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.95e+01 chirality pdb=" CA GLU B 174 " pdb=" N GLU B 174 " pdb=" C GLU B 174 " pdb=" CB GLU B 174 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.76e+00 chirality pdb=" C14 CLR A1101 " pdb=" C13 CLR A1101 " pdb=" C15 CLR A1101 " pdb=" C8 CLR A1101 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.86e+00 ... (remaining 923 not shown) Planarity restraints: 987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB2 CRO B 68 " 0.034 2.00e-02 2.50e+03 2.28e-02 1.30e+01 pdb=" CG2 CRO B 68 " -0.051 2.00e-02 2.50e+03 pdb=" C1 CRO B 68 " 0.004 2.00e-02 2.50e+03 pdb=" C2 CRO B 68 " 0.004 2.00e-02 2.50e+03 pdb=" CA1 CRO B 68 " -0.001 2.00e-02 2.50e+03 pdb=" CA2 CRO B 68 " 0.020 2.00e-02 2.50e+03 pdb=" CA3 CRO B 68 " -0.025 2.00e-02 2.50e+03 pdb=" N2 CRO B 68 " 0.019 2.00e-02 2.50e+03 pdb=" N3 CRO B 68 " -0.005 2.00e-02 2.50e+03 pdb=" O2 CRO B 68 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 90 " -0.046 5.00e-02 4.00e+02 7.01e-02 7.87e+00 pdb=" N PRO B 91 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 91 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 91 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 232 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C ASN C 232 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN C 232 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA C 233 " 0.016 2.00e-02 2.50e+03 ... (remaining 984 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 1997 2.88 - 3.38: 5097 3.38 - 3.89: 8521 3.89 - 4.39: 9456 4.39 - 4.90: 16954 Nonbonded interactions: 42025 Sorted by model distance: nonbonded pdb=" OD1 ASP C 202 " pdb=" N TYR C 206 " model vdw 2.373 3.120 nonbonded pdb=" O ALA A 101 " pdb=" OG SER A 105 " model vdw 2.377 3.040 nonbonded pdb=" N ASP C 235 " pdb=" O ASP C 235 " model vdw 2.403 2.496 nonbonded pdb=" OG1 THR C 70 " pdb=" ND1 HIS C 73 " model vdw 2.410 3.120 nonbonded pdb=" O SER B 88 " pdb=" OG SER B 88 " model vdw 2.428 3.040 ... (remaining 42020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.610 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 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 : 0.008 0.130 5795 Z= 0.492 Angle : 0.985 16.366 7873 Z= 0.554 Chirality : 0.072 1.087 926 Planarity : 0.006 0.070 987 Dihedral : 13.148 86.182 2095 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.29), residues: 704 helix: 0.57 (0.26), residues: 367 sheet: 1.25 (0.47), residues: 113 loop : -2.06 (0.33), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 45 TYR 0.016 0.002 TYR A 176 PHE 0.036 0.002 PHE C 239 TRP 0.015 0.002 TRP A 126 HIS 0.004 0.001 HIS C 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00762 / 0.48 ( 5792) covalent geometry : angle 0.98560 / 0.55 ( 7871) SS BOND : bond 0.01959 / 1.22 ( 1) SS BOND : angle 0.34868 / 0.13 ( 2) hydrogen bonds : bond 0.18849 / 12.06 ( 329) hydrogen bonds : angle 5.95478 / 4.28 ( 957) Misc. bond : bond 0.05280 / 3.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.262 Fit side-chains REVERT: B 126 GLU cc_start: 0.7351 (tt0) cc_final: 0.7026 (tt0) REVERT: B 128 LYS cc_start: 0.7817 (mtmm) cc_final: 0.7477 (mmmt) REVERT: B 164 LYS cc_start: 0.6163 (mttt) cc_final: 0.5884 (ptmm) REVERT: C 239 PHE cc_start: 0.6805 (m-80) cc_final: 0.6601 (m-80) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.0706 time to fit residues: 13.8347 Evaluate side-chains 71 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 27] chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 281 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.200645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.144708 restraints weight = 7172.967| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.82 r_work: 0.3360 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5795 Z= 0.161 Angle : 0.690 9.762 7873 Z= 0.351 Chirality : 0.044 0.184 926 Planarity : 0.005 0.051 987 Dihedral : 5.577 45.709 823 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.00 % Allowed : 11.31 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.30), residues: 704 helix: 0.84 (0.25), residues: 371 sheet: 1.37 (0.47), residues: 111 loop : -1.78 (0.35), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 32 TYR 0.021 0.002 TYR A 176 PHE 0.027 0.002 PHE A 94 TRP 0.021 0.002 TRP A 126 HIS 0.007 0.001 HIS C 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 5792) covalent geometry : angle 0.68959 / 0.35 ( 7871) SS BOND : bond 0.00194 / 0.12 ( 1) SS BOND : angle 0.26919 / 0.13 ( 2) hydrogen bonds : bond 0.05259 / 3.48 ( 329) hydrogen bonds : angle 4.80733 / 3.55 ( 957) Misc. bond : bond 0.00103 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.214 Fit side-chains REVERT: A 80 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.4915 (t80) REVERT: A 115 VAL cc_start: 0.7570 (t) cc_final: 0.7316 (t) REVERT: A 131 CYS cc_start: 0.7535 (t) cc_final: 0.7077 (m) REVERT: A 223 MET cc_start: 0.7358 (ttt) cc_final: 0.6936 (ttm) REVERT: B 5 LYS cc_start: 0.6354 (ptmt) cc_final: 0.6020 (ptpt) REVERT: B 107 THR cc_start: 0.7879 (p) cc_final: 0.7659 (t) REVERT: B 109 LYS cc_start: 0.8055 (mmtm) cc_final: 0.7608 (mmtm) REVERT: B 155 MET cc_start: 0.8293 (tpp) cc_final: 0.7926 (tpp) REVERT: B 164 LYS cc_start: 0.6877 (mttt) cc_final: 0.6437 (ptmm) REVERT: C 236 GLN cc_start: 0.6422 (mt0) cc_final: 0.6011 (mt0) outliers start: 18 outliers final: 12 residues processed: 101 average time/residue: 0.0777 time to fit residues: 10.3466 Evaluate side-chains 85 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 41 TYR Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: [44, 35, 28, 23, 70, 58, 59, 33, 60, 12, 10] chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.197343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.139231 restraints weight = 7108.869| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.81 r_work: 0.3337 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5795 Z= 0.145 Angle : 0.626 6.839 7873 Z= 0.322 Chirality : 0.042 0.202 926 Planarity : 0.005 0.045 987 Dihedral : 5.281 38.238 823 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.16 % Allowed : 13.81 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.30), residues: 704 helix: 1.22 (0.25), residues: 375 sheet: 1.26 (0.47), residues: 113 loop : -1.68 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 111 TYR 0.018 0.002 TYR C 57 PHE 0.018 0.002 PHE A 94 TRP 0.015 0.002 TRP A 126 HIS 0.005 0.001 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 5792) covalent geometry : angle 0.62584 / 0.32 ( 7871) SS BOND : bond 0.00127 / 0.08 ( 1) SS BOND : angle 0.48163 / 0.19 ( 2) hydrogen bonds : bond 0.04929 / 3.27 ( 329) hydrogen bonds : angle 4.59932 / 3.39 ( 957) Misc. bond : bond 0.00038 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.202 Fit side-chains REVERT: A 131 CYS cc_start: 0.7490 (t) cc_final: 0.7035 (m) REVERT: A 1028 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8179 (tt) REVERT: A 223 MET cc_start: 0.7489 (ttt) cc_final: 0.7255 (ttt) REVERT: B 5 LYS cc_start: 0.6497 (ptmt) cc_final: 0.6174 (ptpt) REVERT: B 116 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.8211 (t80) REVERT: B 128 LYS cc_start: 0.7369 (mtmm) cc_final: 0.6869 (mmmt) REVERT: B 158 LYS cc_start: 0.7528 (tppt) cc_final: 0.7029 (mtmm) REVERT: B 164 LYS cc_start: 0.6886 (mttt) cc_final: 0.6444 (ptmm) REVERT: C 22 MET cc_start: 0.5752 (tmm) cc_final: 0.5444 (tmm) REVERT: C 193 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6329 (mmtm) REVERT: C 242 LEU cc_start: 0.7664 (mt) cc_final: 0.7408 (mp) outliers start: 19 outliers final: 11 residues processed: 93 average time/residue: 0.0775 time to fit residues: 9.4147 Evaluate side-chains 83 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 41 TYR Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: [10, 29, 37, 20, 5, 35, 1, 3, 39, 33, 40] chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.194156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.139089 restraints weight = 7127.701| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.50 r_work: 0.3337 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5795 Z= 0.138 Angle : 0.592 6.928 7873 Z= 0.307 Chirality : 0.041 0.211 926 Planarity : 0.004 0.045 987 Dihedral : 5.179 40.597 823 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.83 % Allowed : 15.14 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.31), residues: 704 helix: 1.42 (0.26), residues: 375 sheet: 1.22 (0.46), residues: 113 loop : -1.49 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 32 TYR 0.014 0.002 TYR A 176 PHE 0.016 0.002 PHE A 94 TRP 0.019 0.002 TRP A 126 HIS 0.005 0.001 HIS C 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 5792) covalent geometry : angle 0.59244 / 0.31 ( 7871) SS BOND : bond 0.00522 / 0.33 ( 1) SS BOND : angle 0.55752 / 0.19 ( 2) hydrogen bonds : bond 0.04634 / 3.06 ( 329) hydrogen bonds : angle 4.45576 / 3.30 ( 957) Misc. bond : bond 0.00049 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.227 Fit side-chains REVERT: A 131 CYS cc_start: 0.7573 (t) cc_final: 0.7203 (m) REVERT: A 1028 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8252 (tt) REVERT: A 212 PHE cc_start: 0.6231 (OUTLIER) cc_final: 0.5940 (t80) REVERT: A 223 MET cc_start: 0.7484 (ttt) cc_final: 0.6666 (tpp) REVERT: B 5 LYS cc_start: 0.6778 (ptmt) cc_final: 0.6505 (ptpt) REVERT: B 116 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8170 (t80) REVERT: B 128 LYS cc_start: 0.7431 (mtmm) cc_final: 0.6887 (mmmt) REVERT: B 158 LYS cc_start: 0.7590 (tppt) cc_final: 0.7139 (mtmm) REVERT: C 22 MET cc_start: 0.5884 (tmm) cc_final: 0.5503 (tmm) REVERT: C 193 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6649 (mmtm) REVERT: C 242 LEU cc_start: 0.8060 (mt) cc_final: 0.7778 (mp) outliers start: 23 outliers final: 14 residues processed: 91 average time/residue: 0.0789 time to fit residues: 9.3710 Evaluate side-chains 84 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 41 TYR Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: [16, 29, 45, 60, 70, 57, 47, 17, 36, 30, 64] chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.0270 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.196577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.137817 restraints weight = 7267.126| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.57 r_work: 0.3294 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5795 Z= 0.129 Angle : 0.568 6.704 7873 Z= 0.294 Chirality : 0.040 0.210 926 Planarity : 0.004 0.044 987 Dihedral : 5.111 43.086 823 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.00 % Allowed : 16.97 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.31), residues: 704 helix: 1.58 (0.26), residues: 375 sheet: 1.32 (0.46), residues: 113 loop : -1.39 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 32 TYR 0.012 0.001 TYR A 176 PHE 0.014 0.001 PHE A 94 TRP 0.027 0.002 TRP A 126 HIS 0.004 0.001 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 5792) covalent geometry : angle 0.56764 / 0.29 ( 7871) SS BOND : bond 0.00813 / 0.51 ( 1) SS BOND : angle 0.39215 / 0.14 ( 2) hydrogen bonds : bond 0.04292 / 2.84 ( 329) hydrogen bonds : angle 4.32868 / 3.21 ( 957) Misc. bond : bond 0.00034 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.205 Fit side-chains REVERT: A 131 CYS cc_start: 0.7613 (t) cc_final: 0.7229 (m) REVERT: A 1028 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8206 (tt) REVERT: A 212 PHE cc_start: 0.6251 (OUTLIER) cc_final: 0.5986 (t80) REVERT: A 223 MET cc_start: 0.7453 (ttt) cc_final: 0.6663 (tpp) REVERT: B 5 LYS cc_start: 0.6698 (ptmt) cc_final: 0.6344 (ptpt) REVERT: B 116 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8164 (t80) REVERT: B 128 LYS cc_start: 0.7385 (mtmm) cc_final: 0.6836 (mmmt) REVERT: B 158 LYS cc_start: 0.7633 (tppt) cc_final: 0.7179 (mtmm) REVERT: C 22 MET cc_start: 0.5913 (tmm) cc_final: 0.5636 (tmm) REVERT: C 193 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6890 (mttp) REVERT: C 242 LEU cc_start: 0.7831 (mt) cc_final: 0.7565 (mp) REVERT: C 269 LYS cc_start: 0.6232 (mttt) cc_final: 0.5969 (mmmt) outliers start: 18 outliers final: 11 residues processed: 84 average time/residue: 0.0859 time to fit residues: 9.3321 Evaluate side-chains 84 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 41 TYR Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: [1, 21, 69, 25, 3, 24, 64, 38, 22, 37, 18] chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.193706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134550 restraints weight = 7223.980| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.56 r_work: 0.3267 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5795 Z= 0.144 Angle : 0.591 7.391 7873 Z= 0.306 Chirality : 0.041 0.217 926 Planarity : 0.004 0.045 987 Dihedral : 5.165 44.536 823 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.16 % Allowed : 16.97 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.31), residues: 704 helix: 1.60 (0.26), residues: 375 sheet: 1.31 (0.47), residues: 113 loop : -1.38 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 32 TYR 0.013 0.001 TYR B 94 PHE 0.015 0.001 PHE B 116 TRP 0.019 0.002 TRP A 126 HIS 0.005 0.001 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 5792) covalent geometry : angle 0.59060 / 0.31 ( 7871) SS BOND : bond 0.00273 / 0.17 ( 1) SS BOND : angle 0.49900 / 0.17 ( 2) hydrogen bonds : bond 0.04601 / 3.05 ( 329) hydrogen bonds : angle 4.34127 / 3.22 ( 957) Misc. bond : bond 0.00044 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.140 Fit side-chains REVERT: A 131 CYS cc_start: 0.7702 (t) cc_final: 0.7321 (m) REVERT: A 141 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7948 (tp) REVERT: A 1028 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8296 (tt) REVERT: A 212 PHE cc_start: 0.6268 (OUTLIER) cc_final: 0.6007 (t80) REVERT: A 223 MET cc_start: 0.7459 (ttt) cc_final: 0.6652 (mmt) REVERT: B 5 LYS cc_start: 0.6954 (ptmt) cc_final: 0.6587 (ptpt) REVERT: B 75 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8211 (ttm-80) REVERT: B 116 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8193 (t80) REVERT: B 128 LYS cc_start: 0.7427 (mtmm) cc_final: 0.6863 (mmmt) REVERT: B 158 LYS cc_start: 0.7675 (tppt) cc_final: 0.7228 (mtmm) REVERT: C 193 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6834 (mmtm) REVERT: C 242 LEU cc_start: 0.7846 (mt) cc_final: 0.7584 (mp) REVERT: C 269 LYS cc_start: 0.6156 (mttt) cc_final: 0.5938 (mmmt) outliers start: 25 outliers final: 16 residues processed: 90 average time/residue: 0.0805 time to fit residues: 9.4679 Evaluate side-chains 89 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 41 TYR Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: [63, 9, 53, 28, 51, 34, 65, 27, 38, 29, 39] chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1037 GLN C 184 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.194176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.137031 restraints weight = 7345.986| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.94 r_work: 0.3320 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5795 Z= 0.136 Angle : 0.598 10.109 7873 Z= 0.304 Chirality : 0.041 0.214 926 Planarity : 0.004 0.045 987 Dihedral : 5.148 46.418 823 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.83 % Allowed : 17.47 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.31), residues: 704 helix: 1.61 (0.26), residues: 378 sheet: 1.32 (0.47), residues: 113 loop : -1.36 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 32 TYR 0.011 0.001 TYR B 94 PHE 0.014 0.001 PHE A 104 TRP 0.019 0.002 TRP A 126 HIS 0.005 0.001 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 5792) covalent geometry : angle 0.59763 / 0.30 ( 7871) SS BOND : bond 0.00170 / 0.11 ( 1) SS BOND : angle 0.46937 / 0.17 ( 2) hydrogen bonds : bond 0.04380 / 2.89 ( 329) hydrogen bonds : angle 4.31261 / 3.20 ( 957) Misc. bond : bond 0.00046 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.155 Fit side-chains REVERT: A 131 CYS cc_start: 0.7691 (t) cc_final: 0.7306 (m) REVERT: A 141 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7898 (tp) REVERT: A 1028 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8290 (tt) REVERT: A 212 PHE cc_start: 0.6127 (OUTLIER) cc_final: 0.5869 (t80) REVERT: A 223 MET cc_start: 0.7421 (ttt) cc_final: 0.7106 (ttm) REVERT: B 5 LYS cc_start: 0.6800 (ptmt) cc_final: 0.6456 (ptpt) REVERT: B 116 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8123 (t80) REVERT: B 128 LYS cc_start: 0.7359 (mtmm) cc_final: 0.6800 (mmmt) REVERT: B 158 LYS cc_start: 0.7712 (tppt) cc_final: 0.7248 (mtmm) REVERT: C 22 MET cc_start: 0.6057 (tmm) cc_final: 0.5729 (tmm) REVERT: C 27 ASP cc_start: 0.6622 (t0) cc_final: 0.6409 (t70) REVERT: C 193 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6834 (mmtm) REVERT: C 242 LEU cc_start: 0.7835 (mt) cc_final: 0.7567 (mp) outliers start: 29 outliers final: 19 residues processed: 92 average time/residue: 0.0769 time to fit residues: 9.2018 Evaluate side-chains 90 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 217 TRP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 41 TYR Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: [11, 59, 17, 23, 67, 35, 55, 20, 45, 51, 42] chunk 11 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.192367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.133585 restraints weight = 7196.871| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.54 r_work: 0.3281 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5795 Z= 0.147 Angle : 0.623 10.473 7873 Z= 0.315 Chirality : 0.041 0.205 926 Planarity : 0.004 0.045 987 Dihedral : 5.191 48.105 823 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.99 % Allowed : 17.80 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.31), residues: 704 helix: 1.58 (0.26), residues: 377 sheet: 1.23 (0.47), residues: 113 loop : -1.35 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 32 TYR 0.012 0.001 TYR B 94 PHE 0.014 0.001 PHE A 104 TRP 0.019 0.002 TRP A 126 HIS 0.005 0.001 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 5792) covalent geometry : angle 0.62300 / 0.31 ( 7871) SS BOND : bond 0.00088 / 0.05 ( 1) SS BOND : angle 0.43545 / 0.15 ( 2) hydrogen bonds : bond 0.04582 / 3.03 ( 329) hydrogen bonds : angle 4.37072 / 3.24 ( 957) Misc. bond : bond 0.00043 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.235 Fit side-chains REVERT: A 131 CYS cc_start: 0.7693 (t) cc_final: 0.7316 (m) REVERT: A 141 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7908 (tp) REVERT: A 1021 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8283 (mmmt) REVERT: A 1028 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8311 (tt) REVERT: A 212 PHE cc_start: 0.6203 (OUTLIER) cc_final: 0.5959 (t80) REVERT: A 223 MET cc_start: 0.7440 (ttt) cc_final: 0.7007 (ttm) REVERT: B 5 LYS cc_start: 0.7068 (ptmt) cc_final: 0.6685 (ptpt) REVERT: B 75 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8219 (ttm-80) REVERT: B 116 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8207 (t80) REVERT: B 128 LYS cc_start: 0.7503 (mtmm) cc_final: 0.6891 (mtpt) REVERT: B 158 LYS cc_start: 0.7715 (tppt) cc_final: 0.7264 (mtmm) REVERT: C 22 MET cc_start: 0.6106 (tmm) cc_final: 0.5885 (tmm) REVERT: C 27 ASP cc_start: 0.6714 (t0) cc_final: 0.6492 (t70) REVERT: C 193 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6852 (mmtm) REVERT: C 242 LEU cc_start: 0.7840 (mt) cc_final: 0.7574 (mp) outliers start: 24 outliers final: 17 residues processed: 87 average time/residue: 0.0866 time to fit residues: 9.6718 Evaluate side-chains 90 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 217 TRP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 41 TYR Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: [29, 26, 5, 54, 2, 16, 15, 7, 35, 12, 68] chunk 29 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.195314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.137329 restraints weight = 7230.985| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.51 r_work: 0.3312 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5795 Z= 0.122 Angle : 0.603 13.440 7873 Z= 0.299 Chirality : 0.041 0.208 926 Planarity : 0.004 0.045 987 Dihedral : 5.154 51.689 823 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.99 % Allowed : 18.30 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.31), residues: 704 helix: 1.66 (0.27), residues: 377 sheet: 1.21 (0.47), residues: 113 loop : -1.25 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 32 TYR 0.010 0.001 TYR A 176 PHE 0.013 0.001 PHE A 104 TRP 0.018 0.002 TRP A 126 HIS 0.004 0.001 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 5792) covalent geometry : angle 0.60338 / 0.30 ( 7871) SS BOND : bond 0.00078 / 0.05 ( 1) SS BOND : angle 0.43547 / 0.16 ( 2) hydrogen bonds : bond 0.04039 / 2.65 ( 329) hydrogen bonds : angle 4.26718 / 3.16 ( 957) Misc. bond : bond 0.00043 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.202 Fit side-chains REVERT: A 131 CYS cc_start: 0.7682 (t) cc_final: 0.7349 (m) REVERT: A 141 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7938 (tp) REVERT: A 1028 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8282 (tt) REVERT: A 212 PHE cc_start: 0.6235 (OUTLIER) cc_final: 0.5996 (t80) REVERT: B 5 LYS cc_start: 0.6857 (ptmt) cc_final: 0.6526 (ptpt) REVERT: B 75 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8198 (ttm-80) REVERT: B 116 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8091 (t80) REVERT: B 128 LYS cc_start: 0.7457 (mtmm) cc_final: 0.6900 (mmmt) REVERT: B 158 LYS cc_start: 0.7709 (tppt) cc_final: 0.7229 (mtmm) REVERT: C 27 ASP cc_start: 0.6768 (t0) cc_final: 0.6536 (t70) REVERT: C 193 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.6862 (mmtm) REVERT: C 242 LEU cc_start: 0.7841 (mt) cc_final: 0.7577 (mp) REVERT: C 255 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6211 (mt-10) outliers start: 24 outliers final: 17 residues processed: 87 average time/residue: 0.0762 time to fit residues: 8.6766 Evaluate side-chains 88 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 217 TRP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 41 TYR Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: [7, 10, 4, 32, 68, 3, 11, 38, 47, 16, 57] chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.194974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137277 restraints weight = 7250.194| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.52 r_work: 0.3308 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5795 Z= 0.122 Angle : 0.616 13.168 7873 Z= 0.305 Chirality : 0.041 0.213 926 Planarity : 0.004 0.045 987 Dihedral : 5.145 54.101 823 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.83 % Allowed : 18.64 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.31), residues: 704 helix: 1.66 (0.26), residues: 377 sheet: 1.23 (0.47), residues: 113 loop : -1.24 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 32 TYR 0.013 0.001 TYR C 57 PHE 0.013 0.001 PHE A 104 TRP 0.017 0.002 TRP A 126 HIS 0.004 0.001 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5792) covalent geometry : angle 0.61641 / 0.30 ( 7871) SS BOND : bond 0.00084 / 0.05 ( 1) SS BOND : angle 0.46679 / 0.17 ( 2) hydrogen bonds : bond 0.04034 / 2.63 ( 329) hydrogen bonds : angle 4.26106 / 3.17 ( 957) Misc. bond : bond 0.00038 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1408 Ramachandran restraints generated. 704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.211 Fit side-chains REVERT: A 131 CYS cc_start: 0.7686 (t) cc_final: 0.7341 (m) REVERT: A 141 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7891 (tp) REVERT: A 1028 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8209 (tt) REVERT: A 212 PHE cc_start: 0.6196 (OUTLIER) cc_final: 0.5972 (t80) REVERT: B 5 LYS cc_start: 0.7013 (ptmt) cc_final: 0.6673 (ptpt) REVERT: B 75 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8251 (ttm-80) REVERT: B 116 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8149 (t80) REVERT: B 128 LYS cc_start: 0.7461 (mtmm) cc_final: 0.6908 (mmmt) REVERT: B 158 LYS cc_start: 0.7705 (tppt) cc_final: 0.7236 (mtmm) REVERT: C 27 ASP cc_start: 0.6626 (t0) cc_final: 0.6391 (t70) REVERT: C 193 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6967 (mttp) REVERT: C 242 LEU cc_start: 0.7875 (mt) cc_final: 0.7607 (mp) REVERT: C 255 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6204 (mt-10) outliers start: 23 outliers final: 17 residues processed: 84 average time/residue: 0.0886 time to fit residues: 9.5224 Evaluate side-chains 87 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 217 TRP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 41 TYR Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: [55, 14, 18, 24, 8, 42, 40, 38, 17, 35, 10] chunk 55 optimal weight: 0.9980 chunk 14 optimal weight: 0.0370 chunk 18 optimal weight: 0.0170 chunk 24 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.197486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.140612 restraints weight = 7101.204| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.49 r_work: 0.3354 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5795 Z= 0.105 Angle : 0.581 12.465 7873 Z= 0.283 Chirality : 0.039 0.207 926 Planarity : 0.004 0.045 987 Dihedral : 5.105 57.800 823 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.33 % Allowed : 19.47 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.32), residues: 704 helix: 1.81 (0.27), residues: 378 sheet: 1.40 (0.47), residues: 111 loop : -0.96 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 32 TYR 0.017 0.001 TYR C 57 PHE 0.012 0.001 PHE A 104 TRP 0.015 0.001 TRP A 126 HIS 0.004 0.001 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 5792) covalent geometry : angle 0.58059 / 0.28 ( 7871) SS BOND : bond 0.00070 / 0.04 ( 1) SS BOND : angle 0.45600 / 0.18 ( 2) hydrogen bonds : bond 0.03406 / 2.22 ( 329) hydrogen bonds : angle 4.09815 / 3.04 ( 957) Misc. bond : bond 0.00018 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1564.34 seconds wall clock time: 27 minutes 21.43 seconds (1641.43 seconds total)