Starting phenix.real_space_refine on Sat Aug 23 05:07:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bri_16215/08_2025/8bri_16215.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bri_16215/08_2025/8bri_16215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bri_16215/08_2025/8bri_16215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bri_16215/08_2025/8bri_16215.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bri_16215/08_2025/8bri_16215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bri_16215/08_2025/8bri_16215.map" } resolution = 3.9 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= 0.000 sd= 0.028 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 92 5.16 5 C 6392 2.51 5 N 1625 2.21 5 O 1802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9911 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1880 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 6, 'TRANS': 243} Chain: "B" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1761 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain: "C" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1888 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 6, 'TRANS': 244} Chain: "D" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1825 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 6, 'TRANS': 236} Chain: "E" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1761 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain: "F" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 398 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "G" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 398 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Time building chain proxies: 3.01, per 1000 atoms: 0.30 Number of scatterers: 9911 At special positions: 0 Unit cell: (99.008, 109.824, 113.152, 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 92 16.00 O 1802 8.00 N 1625 7.00 C 6392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 418.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2362 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 1 sheets defined 87.8% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 Processing helix chain 'A' and resid 31 through 48 Processing helix chain 'A' and resid 51 through 68 Processing helix chain 'A' and resid 74 through 91 Processing helix chain 'A' and resid 92 through 95 Processing helix chain 'A' and resid 102 through 115 removed outlier: 3.918A pdb=" N ASP A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 167 removed outlier: 3.578A pdb=" N VAL A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 174 through 196 removed outlier: 4.006A pdb=" N THR A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 228 Processing helix chain 'A' and resid 230 through 240 removed outlier: 3.761A pdb=" N ILE A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 246 through 251 removed outlier: 3.551A pdb=" N ILE A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 50 Processing helix chain 'B' and resid 51 through 68 Processing helix chain 'B' and resid 72 through 90 Processing helix chain 'B' and resid 93 through 98 removed outlier: 3.945A pdb=" N GLU B 96 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET B 98 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 114 Processing helix chain 'B' and resid 117 through 168 Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 171 through 196 removed outlier: 3.586A pdb=" N GLY B 176 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix removed outlier: 3.554A pdb=" N THR B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 227 Processing helix chain 'B' and resid 230 through 240 Processing helix chain 'B' and resid 241 through 244 removed outlier: 3.805A pdb=" N GLU B 244 " --> pdb=" O TYR B 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 241 through 244' Processing helix chain 'B' and resid 245 through 251 removed outlier: 3.946A pdb=" N LEU B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 24 Processing helix chain 'C' and resid 31 through 50 removed outlier: 3.743A pdb=" N LYS C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 68 Processing helix chain 'C' and resid 72 through 91 Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.875A pdb=" N GLU C 96 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU C 97 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 Processing helix chain 'C' and resid 117 through 168 Proline residue: C 151 - end of helix Processing helix chain 'C' and resid 175 through 196 removed outlier: 4.013A pdb=" N THR C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 228 Processing helix chain 'C' and resid 230 through 246 Processing helix chain 'D' and resid 2 through 23 removed outlier: 3.654A pdb=" N GLY D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 30 removed outlier: 3.582A pdb=" N VAL D 30 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 47 Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 72 through 90 removed outlier: 3.519A pdb=" N LEU D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.545A pdb=" N GLU D 96 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 114 Processing helix chain 'D' and resid 117 through 168 Proline residue: D 151 - end of helix removed outlier: 3.865A pdb=" N ASN D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 196 removed outlier: 3.557A pdb=" N ALA D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR D 185 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 228 Processing helix chain 'D' and resid 230 through 243 Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.600A pdb=" N MET E 28 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 48 Processing helix chain 'E' and resid 51 through 68 Processing helix chain 'E' and resid 72 through 91 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 117 through 168 Proline residue: E 151 - end of helix Processing helix chain 'E' and resid 171 through 196 Proline residue: E 177 - end of helix removed outlier: 3.704A pdb=" N THR E 186 " --> pdb=" O ALA E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 227 Processing helix chain 'E' and resid 230 through 243 removed outlier: 3.671A pdb=" N SER E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR E 241 " --> pdb=" O TYR E 237 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU E 242 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN E 243 " --> pdb=" O LYS E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 250 removed outlier: 3.591A pdb=" N ALA E 248 " --> pdb=" O GLY E 245 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU E 249 " --> pdb=" O LYS E 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 39 removed outlier: 3.886A pdb=" N GLY F 20 " --> pdb=" O PRO F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 58 removed outlier: 3.666A pdb=" N LYS F 48 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 39 removed outlier: 4.523A pdb=" N THR G 21 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE G 39 " --> pdb=" O LEU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 58 Processing sheet with id=AA1, first strand: chain 'F' and resid 40 through 42 868 hydrogen bonds defined for protein. 2574 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1778 1.32 - 1.45: 2242 1.45 - 1.57: 5854 1.57 - 1.70: 0 1.70 - 1.82: 182 Bond restraints: 10056 Sorted by residual: bond pdb=" CG GLN D 210 " pdb=" CD GLN D 210 " ideal model delta sigma weight residual 1.516 1.459 0.057 2.50e-02 1.60e+03 5.14e+00 bond pdb=" CB ILE D 156 " pdb=" CG2 ILE D 156 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.34e+00 bond pdb=" CB VAL G 34 " pdb=" CG1 VAL G 34 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.03e+00 bond pdb=" CG MET F 30 " pdb=" SD MET F 30 " ideal model delta sigma weight residual 1.803 1.756 0.047 2.50e-02 1.60e+03 3.54e+00 bond pdb=" CG MET A 169 " pdb=" SD MET A 169 " ideal model delta sigma weight residual 1.803 1.756 0.047 2.50e-02 1.60e+03 3.49e+00 ... (remaining 10051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.31: 13307 4.31 - 8.63: 190 8.63 - 12.94: 31 12.94 - 17.26: 12 17.26 - 21.57: 1 Bond angle restraints: 13541 Sorted by residual: angle pdb=" O PHE F 58 " pdb=" C PHE F 58 " pdb=" N GLY F 59 " ideal model delta sigma weight residual 122.19 100.62 21.57 1.21e+00 6.83e-01 3.18e+02 angle pdb=" CA MET B 219 " pdb=" CB MET B 219 " pdb=" CG MET B 219 " ideal model delta sigma weight residual 114.10 128.24 -14.14 2.00e+00 2.50e-01 5.00e+01 angle pdb=" CA MET D 83 " pdb=" CB MET D 83 " pdb=" CG MET D 83 " ideal model delta sigma weight residual 114.10 128.10 -14.00 2.00e+00 2.50e-01 4.90e+01 angle pdb=" CA MET C 219 " pdb=" CB MET C 219 " pdb=" CG MET C 219 " ideal model delta sigma weight residual 114.10 127.70 -13.60 2.00e+00 2.50e-01 4.62e+01 angle pdb=" CA MET C 83 " pdb=" CB MET C 83 " pdb=" CG MET C 83 " ideal model delta sigma weight residual 114.10 126.60 -12.50 2.00e+00 2.50e-01 3.90e+01 ... (remaining 13536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5201 17.64 - 35.28: 670 35.28 - 52.92: 152 52.92 - 70.56: 18 70.56 - 88.20: 15 Dihedral angle restraints: 6056 sinusoidal: 2374 harmonic: 3682 Sorted by residual: dihedral pdb=" CA GLU D 99 " pdb=" C GLU D 99 " pdb=" N ILE D 100 " pdb=" CA ILE D 100 " ideal model delta harmonic sigma weight residual -180.00 -154.69 -25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" N GLN D 210 " pdb=" C GLN D 210 " pdb=" CA GLN D 210 " pdb=" CB GLN D 210 " ideal model delta harmonic sigma weight residual 122.80 133.25 -10.45 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" N MET E 83 " pdb=" C MET E 83 " pdb=" CA MET E 83 " pdb=" CB MET E 83 " ideal model delta harmonic sigma weight residual 122.80 133.11 -10.31 0 2.50e+00 1.60e-01 1.70e+01 ... (remaining 6053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1506 0.122 - 0.243: 73 0.243 - 0.365: 15 0.365 - 0.487: 1 0.487 - 0.608: 1 Chirality restraints: 1596 Sorted by residual: chirality pdb=" CB ILE C 100 " pdb=" CA ILE C 100 " pdb=" CG1 ILE C 100 " pdb=" CG2 ILE C 100 " both_signs ideal model delta sigma weight residual False 2.64 2.04 0.61 2.00e-01 2.50e+01 9.25e+00 chirality pdb=" CG LEU D 213 " pdb=" CB LEU D 213 " pdb=" CD1 LEU D 213 " pdb=" CD2 LEU D 213 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CG LEU D 166 " pdb=" CB LEU D 166 " pdb=" CD1 LEU D 166 " pdb=" CD2 LEU D 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1593 not shown) Planarity restraints: 1725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE F 58 " 0.089 2.00e-02 2.50e+03 1.54e-01 2.39e+02 pdb=" C PHE F 58 " -0.268 2.00e-02 2.50e+03 pdb=" O PHE F 58 " 0.095 2.00e-02 2.50e+03 pdb=" N GLY F 59 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 58 " 0.037 2.00e-02 2.50e+03 7.20e-02 5.19e+01 pdb=" C PHE G 58 " -0.125 2.00e-02 2.50e+03 pdb=" O PHE G 58 " 0.046 2.00e-02 2.50e+03 pdb=" N GLY G 59 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 44 " -0.024 2.00e-02 2.50e+03 2.80e-02 1.37e+01 pdb=" CG PHE D 44 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE D 44 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE D 44 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE D 44 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE D 44 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 44 " 0.001 2.00e-02 2.50e+03 ... (remaining 1722 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 84 2.55 - 3.14: 8640 3.14 - 3.73: 17280 3.73 - 4.31: 21721 4.31 - 4.90: 35416 Nonbonded interactions: 83141 Sorted by model distance: nonbonded pdb=" OG SER D 193 " pdb=" OD1 ASN D 194 " model vdw 1.969 3.040 nonbonded pdb=" O PHE C 29 " pdb=" OH TYR C 188 " model vdw 2.167 3.040 nonbonded pdb=" O PHE D 29 " pdb=" OH TYR D 188 " model vdw 2.188 3.040 nonbonded pdb=" OD1 ASN E 101 " pdb=" N ASN E 102 " model vdw 2.189 3.120 nonbonded pdb=" NZ LYS C 107 " pdb=" OD2 ASP C 128 " model vdw 2.207 3.120 ... (remaining 83136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 20 through 243) selection = (chain 'B' and resid 20 through 243) selection = (chain 'C' and resid 20 through 243) selection = (chain 'D' and resid 20 through 243) selection = (chain 'E' and resid 20 through 243) } ncs_group { reference = chain 'F' selection = chain 'G' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.660 Find NCS groups from input model: 0.220 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.005 0.069 10056 Z= 0.243 Angle : 1.304 21.571 13541 Z= 0.665 Chirality : 0.066 0.608 1596 Planarity : 0.007 0.154 1725 Dihedral : 16.369 88.201 3694 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.15 % Allowed : 30.13 % Favored : 68.71 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.23), residues: 1298 helix: 1.84 (0.16), residues: 1088 sheet: None (None), residues: 0 loop : -1.03 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 144 TYR 0.042 0.003 TYR B 237 PHE 0.065 0.002 PHE D 44 TRP 0.016 0.004 TRP G 18 HIS 0.003 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00545 (10056) covalent geometry : angle 1.30375 (13541) hydrogen bonds : bond 0.11201 ( 868) hydrogen bonds : angle 5.35186 ( 2574) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 286 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6890 (tm-30) REVERT: B 138 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8432 (mm-40) REVERT: C 169 MET cc_start: 0.7424 (tmm) cc_final: 0.7222 (tmm) REVERT: C 208 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.7957 (ttp-110) REVERT: D 134 GLU cc_start: 0.8411 (pp20) cc_final: 0.7583 (pp20) REVERT: E 39 VAL cc_start: 0.7848 (t) cc_final: 0.7645 (p) REVERT: E 169 MET cc_start: 0.8246 (ppp) cc_final: 0.7884 (ttp) outliers start: 12 outliers final: 4 residues processed: 290 average time/residue: 0.1085 time to fit residues: 43.7773 Evaluate side-chains 269 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 264 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 99 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 ASN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.125128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.093310 restraints weight = 30077.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.095375 restraints weight = 21585.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.097170 restraints weight = 13339.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.097538 restraints weight = 11244.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.097697 restraints weight = 11052.774| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10056 Z= 0.165 Angle : 0.811 10.055 13541 Z= 0.404 Chirality : 0.045 0.245 1596 Planarity : 0.005 0.041 1725 Dihedral : 5.190 59.883 1383 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.13 % Allowed : 21.69 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.23), residues: 1298 helix: 1.49 (0.15), residues: 1104 sheet: None (None), residues: 0 loop : -1.08 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 208 TYR 0.033 0.002 TYR B 237 PHE 0.033 0.002 PHE F 32 TRP 0.010 0.002 TRP G 18 HIS 0.002 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00365 (10056) covalent geometry : angle 0.81122 (13541) hydrogen bonds : bond 0.04431 ( 868) hydrogen bonds : angle 4.49319 ( 2574) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 288 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8754 (mpp) cc_final: 0.8454 (mpp) REVERT: A 98 MET cc_start: 0.4326 (mtp) cc_final: 0.3849 (mtt) REVERT: B 134 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7267 (tm-30) REVERT: B 138 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8805 (mm-40) REVERT: C 56 PHE cc_start: 0.7165 (m-80) cc_final: 0.6872 (m-80) REVERT: D 15 PHE cc_start: 0.8315 (m-80) cc_final: 0.8095 (m-80) REVERT: D 83 MET cc_start: 0.9349 (mmm) cc_final: 0.9084 (mmm) REVERT: D 166 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9139 (mm) REVERT: D 229 GLN cc_start: 0.6842 (OUTLIER) cc_final: 0.6627 (pp30) REVERT: E 68 PHE cc_start: 0.7750 (m-80) cc_final: 0.7375 (m-10) REVERT: E 117 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7726 (p0) REVERT: E 153 MET cc_start: 0.8838 (mmm) cc_final: 0.8479 (tpp) REVERT: E 165 MET cc_start: 0.8409 (mtm) cc_final: 0.8180 (ttm) REVERT: F 19 MET cc_start: 0.8346 (tpt) cc_final: 0.8137 (tpt) outliers start: 43 outliers final: 22 residues processed: 310 average time/residue: 0.1026 time to fit residues: 44.7403 Evaluate side-chains 286 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 261 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 127 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.124166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.092366 restraints weight = 29964.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.094571 restraints weight = 21094.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.096061 restraints weight = 13187.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.096403 restraints weight = 11722.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.096522 restraints weight = 11294.355| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10056 Z= 0.159 Angle : 0.787 12.598 13541 Z= 0.389 Chirality : 0.044 0.225 1596 Planarity : 0.004 0.036 1725 Dihedral : 4.443 54.321 1372 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.61 % Allowed : 23.03 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.23), residues: 1298 helix: 1.41 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -1.16 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 122 TYR 0.024 0.002 TYR B 237 PHE 0.025 0.002 PHE F 39 TRP 0.006 0.002 TRP G 18 HIS 0.002 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00353 (10056) covalent geometry : angle 0.78680 (13541) hydrogen bonds : bond 0.04070 ( 868) hydrogen bonds : angle 4.38026 ( 2574) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 277 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.4170 (mtp) cc_final: 0.3869 (mtt) REVERT: B 134 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7252 (tm-30) REVERT: B 138 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8769 (mm-40) REVERT: B 153 MET cc_start: 0.8579 (tpp) cc_final: 0.7970 (tpp) REVERT: B 169 MET cc_start: 0.7097 (tmm) cc_final: 0.6782 (tmm) REVERT: C 56 PHE cc_start: 0.7250 (m-80) cc_final: 0.6920 (m-10) REVERT: C 208 ARG cc_start: 0.8384 (ttp-110) cc_final: 0.7820 (ttp-110) REVERT: D 15 PHE cc_start: 0.8254 (m-80) cc_final: 0.8051 (m-80) REVERT: D 83 MET cc_start: 0.9413 (mmm) cc_final: 0.9160 (mmm) REVERT: D 211 GLU cc_start: 0.9044 (tp30) cc_final: 0.8619 (tp30) REVERT: E 68 PHE cc_start: 0.7807 (m-80) cc_final: 0.7171 (m-10) REVERT: E 117 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7545 (p0) REVERT: E 153 MET cc_start: 0.8792 (mmm) cc_final: 0.8518 (tpp) REVERT: E 210 GLN cc_start: 0.9129 (mt0) cc_final: 0.8846 (mt0) REVERT: E 214 ASN cc_start: 0.8942 (m110) cc_final: 0.8616 (p0) REVERT: E 218 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8198 (mm) outliers start: 48 outliers final: 28 residues processed: 302 average time/residue: 0.0986 time to fit residues: 42.0656 Evaluate side-chains 289 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 259 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 218 ILE Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 18 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 88 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN B 229 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.123390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.091952 restraints weight = 30409.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.093872 restraints weight = 20583.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.095696 restraints weight = 13529.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.095659 restraints weight = 11472.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.095834 restraints weight = 10876.005| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10056 Z= 0.153 Angle : 0.768 9.159 13541 Z= 0.379 Chirality : 0.043 0.295 1596 Planarity : 0.004 0.035 1725 Dihedral : 4.437 53.236 1372 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.99 % Allowed : 24.09 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.23), residues: 1298 helix: 1.41 (0.15), residues: 1106 sheet: None (None), residues: 0 loop : -1.09 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 122 TYR 0.018 0.002 TYR B 237 PHE 0.025 0.002 PHE F 39 TRP 0.008 0.002 TRP G 18 HIS 0.002 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00340 (10056) covalent geometry : angle 0.76821 (13541) hydrogen bonds : bond 0.03970 ( 868) hydrogen bonds : angle 4.35105 ( 2574) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 284 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.8774 (mpp) cc_final: 0.8454 (mpp) REVERT: A 98 MET cc_start: 0.4151 (mtp) cc_final: 0.3770 (mtt) REVERT: A 134 GLU cc_start: 0.8057 (pp20) cc_final: 0.7747 (pp20) REVERT: A 230 ASN cc_start: 0.8843 (t0) cc_final: 0.8427 (p0) REVERT: B 134 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7231 (tm-30) REVERT: B 138 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8677 (mm-40) REVERT: B 153 MET cc_start: 0.8607 (tpp) cc_final: 0.7975 (tpp) REVERT: C 52 MET cc_start: 0.8408 (tpp) cc_final: 0.8193 (tpp) REVERT: C 56 PHE cc_start: 0.7278 (m-80) cc_final: 0.6982 (m-10) REVERT: C 208 ARG cc_start: 0.8391 (ttp-110) cc_final: 0.7741 (ttp-110) REVERT: D 83 MET cc_start: 0.9418 (mmm) cc_final: 0.9205 (mmm) REVERT: D 105 MET cc_start: 0.8349 (ppp) cc_final: 0.7658 (ppp) REVERT: D 106 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8595 (mm-40) REVERT: D 137 THR cc_start: 0.9193 (p) cc_final: 0.8985 (p) REVERT: D 208 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8285 (ttp80) REVERT: D 211 GLU cc_start: 0.9001 (tp30) cc_final: 0.8720 (tp30) REVERT: D 219 MET cc_start: 0.8926 (ppp) cc_final: 0.8683 (ppp) REVERT: D 226 GLN cc_start: 0.8874 (mm110) cc_final: 0.8547 (mm110) REVERT: E 68 PHE cc_start: 0.7826 (m-80) cc_final: 0.7299 (m-10) REVERT: E 117 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7567 (p0) REVERT: E 153 MET cc_start: 0.8819 (mmm) cc_final: 0.8565 (tpt) REVERT: E 165 MET cc_start: 0.8430 (mtm) cc_final: 0.8179 (ttm) REVERT: E 210 GLN cc_start: 0.9122 (mt0) cc_final: 0.8886 (mt0) REVERT: E 214 ASN cc_start: 0.8973 (m110) cc_final: 0.8585 (p0) REVERT: G 42 MET cc_start: 0.8632 (tmm) cc_final: 0.8412 (tmm) outliers start: 52 outliers final: 36 residues processed: 310 average time/residue: 0.0993 time to fit residues: 43.7353 Evaluate side-chains 299 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 262 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 73 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.121769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.089848 restraints weight = 30343.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.091720 restraints weight = 19546.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.093226 restraints weight = 13307.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.093481 restraints weight = 11574.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.093655 restraints weight = 10971.528| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10056 Z= 0.196 Angle : 0.807 13.154 13541 Z= 0.403 Chirality : 0.044 0.198 1596 Planarity : 0.004 0.033 1725 Dihedral : 4.210 16.733 1369 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 5.37 % Allowed : 24.47 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.23), residues: 1298 helix: 1.34 (0.16), residues: 1107 sheet: None (None), residues: 0 loop : -1.24 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 122 TYR 0.040 0.002 TYR B 237 PHE 0.024 0.002 PHE E 104 TRP 0.010 0.002 TRP G 18 HIS 0.003 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00444 (10056) covalent geometry : angle 0.80745 (13541) hydrogen bonds : bond 0.04027 ( 868) hydrogen bonds : angle 4.48436 ( 2574) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.4148 (mtp) cc_final: 0.3918 (mtt) REVERT: A 230 ASN cc_start: 0.8839 (t0) cc_final: 0.8452 (p0) REVERT: B 134 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7323 (tm-30) REVERT: B 138 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8742 (mm-40) REVERT: B 153 MET cc_start: 0.8605 (tpp) cc_final: 0.7915 (tpp) REVERT: C 61 ILE cc_start: 0.8709 (tp) cc_final: 0.8449 (tp) REVERT: D 105 MET cc_start: 0.8341 (ppp) cc_final: 0.7702 (ppp) REVERT: D 106 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8545 (mm-40) REVERT: D 137 THR cc_start: 0.9191 (p) cc_final: 0.8979 (p) REVERT: D 208 ARG cc_start: 0.8821 (ttp80) cc_final: 0.8202 (ttp80) REVERT: D 211 GLU cc_start: 0.8999 (tp30) cc_final: 0.8507 (tp30) REVERT: D 216 ARG cc_start: 0.9346 (ttt180) cc_final: 0.9107 (tpp80) REVERT: D 219 MET cc_start: 0.8902 (ppp) cc_final: 0.8669 (ppp) REVERT: D 226 GLN cc_start: 0.8877 (mm110) cc_final: 0.8568 (mm110) REVERT: E 68 PHE cc_start: 0.7882 (m-80) cc_final: 0.7319 (m-10) REVERT: E 83 MET cc_start: 0.9032 (mpp) cc_final: 0.8768 (mpp) REVERT: E 117 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7490 (p0) REVERT: E 210 GLN cc_start: 0.9114 (mt0) cc_final: 0.8901 (mt0) REVERT: E 211 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8534 (mm-30) REVERT: E 214 ASN cc_start: 0.8921 (m110) cc_final: 0.8564 (p0) REVERT: E 218 ILE cc_start: 0.8680 (mt) cc_final: 0.8411 (mm) REVERT: F 26 MET cc_start: 0.9300 (mmt) cc_final: 0.9059 (mmm) outliers start: 56 outliers final: 42 residues processed: 313 average time/residue: 0.0984 time to fit residues: 43.7381 Evaluate side-chains 303 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 260 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 0.0770 chunk 116 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN B 229 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.123149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.090611 restraints weight = 30420.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.093167 restraints weight = 17964.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.094856 restraints weight = 13042.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.095458 restraints weight = 10812.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.096375 restraints weight = 9875.821| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10056 Z= 0.153 Angle : 0.806 13.475 13541 Z= 0.399 Chirality : 0.044 0.315 1596 Planarity : 0.004 0.035 1725 Dihedral : 4.260 19.048 1369 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 5.37 % Allowed : 24.95 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.23), residues: 1298 helix: 1.31 (0.16), residues: 1115 sheet: None (None), residues: 0 loop : -1.31 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 122 TYR 0.037 0.002 TYR B 237 PHE 0.024 0.002 PHE F 39 TRP 0.012 0.002 TRP G 18 HIS 0.002 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00343 (10056) covalent geometry : angle 0.80617 (13541) hydrogen bonds : bond 0.03947 ( 868) hydrogen bonds : angle 4.43878 ( 2574) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLU cc_start: 0.8033 (pp20) cc_final: 0.7812 (pp20) REVERT: A 230 ASN cc_start: 0.8798 (t0) cc_final: 0.8539 (p0) REVERT: B 134 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7210 (tm-30) REVERT: B 138 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8620 (mm-40) REVERT: B 153 MET cc_start: 0.8528 (tpp) cc_final: 0.7809 (tpp) REVERT: B 169 MET cc_start: 0.6869 (tmm) cc_final: 0.6427 (tmm) REVERT: B 210 GLN cc_start: 0.8764 (tt0) cc_final: 0.8190 (pp30) REVERT: B 211 GLU cc_start: 0.8688 (tp30) cc_final: 0.8336 (tp30) REVERT: C 56 PHE cc_start: 0.7168 (m-80) cc_final: 0.6823 (m-80) REVERT: C 61 ILE cc_start: 0.8692 (tp) cc_final: 0.8456 (tp) REVERT: C 74 GLU cc_start: 0.8889 (pm20) cc_final: 0.8640 (pm20) REVERT: D 105 MET cc_start: 0.8264 (ppp) cc_final: 0.7682 (ppp) REVERT: D 106 GLN cc_start: 0.9123 (mm110) cc_final: 0.8703 (mm-40) REVERT: D 137 THR cc_start: 0.9166 (p) cc_final: 0.8944 (p) REVERT: D 208 ARG cc_start: 0.8799 (ttp80) cc_final: 0.8152 (ttp80) REVERT: D 211 GLU cc_start: 0.9055 (tp30) cc_final: 0.8723 (tp30) REVERT: D 216 ARG cc_start: 0.9376 (ttt180) cc_final: 0.8976 (tpp80) REVERT: D 226 GLN cc_start: 0.8845 (mm110) cc_final: 0.8546 (mm110) REVERT: E 68 PHE cc_start: 0.7844 (m-80) cc_final: 0.7299 (m-10) REVERT: E 117 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7462 (p0) REVERT: E 211 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8520 (mm-30) REVERT: E 214 ASN cc_start: 0.8984 (m110) cc_final: 0.8630 (p0) REVERT: E 218 ILE cc_start: 0.8610 (mt) cc_final: 0.8324 (mm) REVERT: F 26 MET cc_start: 0.9242 (mmt) cc_final: 0.8997 (mmm) REVERT: G 19 MET cc_start: 0.8665 (tpp) cc_final: 0.8319 (tpp) REVERT: G 42 MET cc_start: 0.8570 (tmm) cc_final: 0.8046 (tmm) outliers start: 56 outliers final: 40 residues processed: 311 average time/residue: 0.0932 time to fit residues: 41.5049 Evaluate side-chains 312 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 129 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 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 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.122386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.090760 restraints weight = 29963.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.093324 restraints weight = 17194.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.095081 restraints weight = 12287.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.095966 restraints weight = 10059.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.096762 restraints weight = 9003.348| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10056 Z= 0.164 Angle : 0.840 12.988 13541 Z= 0.416 Chirality : 0.045 0.261 1596 Planarity : 0.004 0.036 1725 Dihedral : 4.296 18.111 1369 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.37 % Allowed : 25.53 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.23), residues: 1298 helix: 1.28 (0.16), residues: 1117 sheet: None (None), residues: 0 loop : -1.33 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 208 TYR 0.033 0.002 TYR B 237 PHE 0.025 0.002 PHE F 39 TRP 0.007 0.002 TRP G 18 HIS 0.003 0.001 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00374 (10056) covalent geometry : angle 0.83966 (13541) hydrogen bonds : bond 0.03999 ( 868) hydrogen bonds : angle 4.46155 ( 2574) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 278 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.9023 (mmm) cc_final: 0.8635 (mtm) REVERT: B 122 ARG cc_start: 0.9065 (ttp80) cc_final: 0.8789 (ttp80) REVERT: B 134 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7299 (tm-30) REVERT: B 138 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8667 (mm-40) REVERT: B 153 MET cc_start: 0.8557 (tpp) cc_final: 0.7870 (tpp) REVERT: B 169 MET cc_start: 0.6924 (tmm) cc_final: 0.6527 (tmm) REVERT: B 194 ASN cc_start: 0.8029 (m-40) cc_final: 0.7520 (m-40) REVERT: C 56 PHE cc_start: 0.7299 (m-80) cc_final: 0.6971 (m-80) REVERT: C 169 MET cc_start: 0.7732 (tmm) cc_final: 0.7455 (tmm) REVERT: D 105 MET cc_start: 0.8257 (ppp) cc_final: 0.7783 (ppp) REVERT: D 106 GLN cc_start: 0.9106 (mm110) cc_final: 0.8675 (mm-40) REVERT: D 137 THR cc_start: 0.9185 (p) cc_final: 0.8952 (p) REVERT: D 208 ARG cc_start: 0.8823 (ttp80) cc_final: 0.8131 (ttp80) REVERT: D 211 GLU cc_start: 0.9038 (tp30) cc_final: 0.8740 (tp30) REVERT: D 216 ARG cc_start: 0.9356 (ttt180) cc_final: 0.9045 (tpp80) REVERT: D 226 GLN cc_start: 0.8812 (mm110) cc_final: 0.8574 (mm110) REVERT: E 68 PHE cc_start: 0.7805 (m-80) cc_final: 0.7190 (m-10) REVERT: E 105 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8325 (tpp) REVERT: E 117 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7372 (p0) REVERT: E 210 GLN cc_start: 0.9176 (mt0) cc_final: 0.8938 (mp10) REVERT: E 214 ASN cc_start: 0.8997 (m110) cc_final: 0.8701 (p0) REVERT: E 218 ILE cc_start: 0.8669 (mt) cc_final: 0.8202 (mm) REVERT: F 26 MET cc_start: 0.9248 (mmt) cc_final: 0.8996 (mmm) outliers start: 56 outliers final: 44 residues processed: 308 average time/residue: 0.0956 time to fit residues: 42.0624 Evaluate side-chains 316 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 270 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 115 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 55 optimal weight: 0.0070 chunk 98 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN B 229 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.123584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.091770 restraints weight = 30360.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.094290 restraints weight = 17970.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.096007 restraints weight = 13031.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.097036 restraints weight = 10786.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.097547 restraints weight = 9668.766| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10056 Z= 0.158 Angle : 0.877 15.587 13541 Z= 0.427 Chirality : 0.046 0.262 1596 Planarity : 0.004 0.037 1725 Dihedral : 4.350 19.132 1369 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.22 % Allowed : 26.97 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.23), residues: 1298 helix: 1.26 (0.16), residues: 1113 sheet: None (None), residues: 0 loop : -1.21 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 208 TYR 0.031 0.002 TYR B 237 PHE 0.025 0.002 PHE F 39 TRP 0.012 0.002 TRP G 18 HIS 0.002 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00354 (10056) covalent geometry : angle 0.87656 (13541) hydrogen bonds : bond 0.04010 ( 868) hydrogen bonds : angle 4.46790 ( 2574) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 274 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ARG cc_start: 0.9009 (ttp80) cc_final: 0.8784 (ttp80) REVERT: B 134 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7115 (tm-30) REVERT: B 138 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8547 (mm-40) REVERT: B 153 MET cc_start: 0.8522 (tpp) cc_final: 0.7874 (tpp) REVERT: B 169 MET cc_start: 0.6907 (tmm) cc_final: 0.6628 (tmm) REVERT: B 194 ASN cc_start: 0.7903 (m-40) cc_final: 0.7421 (m-40) REVERT: B 210 GLN cc_start: 0.8731 (tt0) cc_final: 0.8237 (pp30) REVERT: B 211 GLU cc_start: 0.8683 (tp30) cc_final: 0.8350 (tp30) REVERT: C 56 PHE cc_start: 0.7242 (m-80) cc_final: 0.6960 (m-80) REVERT: C 74 GLU cc_start: 0.8870 (pm20) cc_final: 0.8648 (pm20) REVERT: D 28 MET cc_start: 0.7441 (ppp) cc_final: 0.6758 (tmm) REVERT: D 99 GLU cc_start: 0.8402 (mp0) cc_final: 0.8028 (pm20) REVERT: D 105 MET cc_start: 0.8297 (ppp) cc_final: 0.7822 (ppp) REVERT: D 106 GLN cc_start: 0.9165 (mm110) cc_final: 0.8722 (mm-40) REVERT: D 134 GLU cc_start: 0.8333 (pp20) cc_final: 0.7505 (pp20) REVERT: D 137 THR cc_start: 0.9158 (p) cc_final: 0.8945 (p) REVERT: D 208 ARG cc_start: 0.8770 (ttp80) cc_final: 0.8080 (ttp80) REVERT: D 211 GLU cc_start: 0.9022 (tp30) cc_final: 0.8706 (tp30) REVERT: D 216 ARG cc_start: 0.9343 (ttt180) cc_final: 0.9048 (tpp80) REVERT: D 226 GLN cc_start: 0.8780 (mm110) cc_final: 0.8545 (mm110) REVERT: E 68 PHE cc_start: 0.7891 (m-80) cc_final: 0.7336 (m-10) REVERT: E 105 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8564 (tpp) REVERT: E 117 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7331 (p0) REVERT: E 210 GLN cc_start: 0.9156 (mt0) cc_final: 0.8767 (mp10) REVERT: E 214 ASN cc_start: 0.8954 (m110) cc_final: 0.8616 (m-40) REVERT: E 218 ILE cc_start: 0.8668 (mt) cc_final: 0.8179 (mm) REVERT: F 26 MET cc_start: 0.9218 (mmt) cc_final: 0.9001 (mmm) outliers start: 44 outliers final: 36 residues processed: 297 average time/residue: 0.0964 time to fit residues: 40.6985 Evaluate side-chains 308 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 93 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 70 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN C 106 GLN ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.123377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.091567 restraints weight = 30491.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.094075 restraints weight = 18145.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.095676 restraints weight = 13221.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.096377 restraints weight = 11000.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.097217 restraints weight = 10009.759| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10056 Z= 0.168 Angle : 0.906 15.064 13541 Z= 0.444 Chirality : 0.047 0.266 1596 Planarity : 0.004 0.037 1725 Dihedral : 4.387 19.366 1369 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.89 % Allowed : 26.49 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.23), residues: 1298 helix: 1.22 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -1.32 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 208 TYR 0.031 0.002 TYR B 237 PHE 0.025 0.002 PHE F 39 TRP 0.007 0.002 TRP F 18 HIS 0.002 0.001 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00381 (10056) covalent geometry : angle 0.90601 (13541) hydrogen bonds : bond 0.04094 ( 868) hydrogen bonds : angle 4.55142 ( 2574) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 278 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 MET cc_start: 0.4813 (mmp) cc_final: 0.4600 (mmp) REVERT: B 72 GLU cc_start: 0.8286 (tp30) cc_final: 0.8041 (tm-30) REVERT: B 122 ARG cc_start: 0.9000 (ttp80) cc_final: 0.8799 (ttp80) REVERT: B 134 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7134 (tm-30) REVERT: B 138 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8537 (mm-40) REVERT: B 153 MET cc_start: 0.8572 (tpp) cc_final: 0.7974 (tpp) REVERT: B 169 MET cc_start: 0.6846 (tmm) cc_final: 0.6634 (tmm) REVERT: B 194 ASN cc_start: 0.7930 (m-40) cc_final: 0.7453 (m-40) REVERT: B 210 GLN cc_start: 0.8689 (tt0) cc_final: 0.8223 (pp30) REVERT: B 211 GLU cc_start: 0.8679 (tp30) cc_final: 0.8349 (tp30) REVERT: C 56 PHE cc_start: 0.7284 (m-80) cc_final: 0.7031 (m-80) REVERT: D 28 MET cc_start: 0.7584 (ppp) cc_final: 0.7030 (ppp) REVERT: D 99 GLU cc_start: 0.8384 (mp0) cc_final: 0.8005 (pm20) REVERT: D 105 MET cc_start: 0.8260 (ppp) cc_final: 0.7875 (ppp) REVERT: D 106 GLN cc_start: 0.9100 (mm110) cc_final: 0.8680 (mm-40) REVERT: D 134 GLU cc_start: 0.8273 (pp20) cc_final: 0.7462 (pp20) REVERT: D 137 THR cc_start: 0.9135 (p) cc_final: 0.8904 (p) REVERT: D 208 ARG cc_start: 0.8803 (ttp80) cc_final: 0.8098 (ttp80) REVERT: D 211 GLU cc_start: 0.9040 (tp30) cc_final: 0.8531 (tp30) REVERT: D 216 ARG cc_start: 0.9340 (ttt180) cc_final: 0.9061 (tpp80) REVERT: D 226 GLN cc_start: 0.8821 (mm110) cc_final: 0.8476 (mm110) REVERT: E 68 PHE cc_start: 0.7907 (m-80) cc_final: 0.6285 (m-80) REVERT: E 105 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8491 (mmm) REVERT: E 117 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7337 (p0) REVERT: E 165 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7650 (mmm) REVERT: E 210 GLN cc_start: 0.9144 (mt0) cc_final: 0.8756 (mp10) REVERT: E 214 ASN cc_start: 0.8954 (m110) cc_final: 0.8617 (m110) REVERT: E 218 ILE cc_start: 0.8684 (mt) cc_final: 0.8339 (mm) outliers start: 51 outliers final: 39 residues processed: 305 average time/residue: 0.0971 time to fit residues: 42.0695 Evaluate side-chains 311 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 269 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.9645 > 50: distance: 35 - 57: 7.551 distance: 43 - 65: 6.566 distance: 47 - 69: 9.849 distance: 51 - 57: 6.924 distance: 52 - 76: 9.631 distance: 57 - 58: 14.575 distance: 58 - 59: 12.673 distance: 58 - 61: 10.270 distance: 59 - 60: 4.683 distance: 59 - 65: 11.494 distance: 60 - 84: 14.304 distance: 61 - 62: 11.594 distance: 62 - 63: 16.040 distance: 62 - 64: 10.746 distance: 65 - 66: 12.113 distance: 66 - 67: 11.358 distance: 67 - 68: 9.160 distance: 67 - 69: 9.756 distance: 68 - 89: 6.261 distance: 69 - 70: 4.237 distance: 70 - 71: 7.423 distance: 70 - 73: 21.292 distance: 71 - 72: 7.244 distance: 71 - 76: 5.459 distance: 72 - 97: 23.510 distance: 73 - 74: 9.507 distance: 73 - 75: 16.047 distance: 76 - 77: 3.286 distance: 77 - 78: 12.375 distance: 77 - 80: 15.218 distance: 78 - 79: 16.275 distance: 78 - 84: 16.686 distance: 79 - 106: 21.308 distance: 80 - 81: 19.301 distance: 81 - 82: 15.322 distance: 81 - 83: 12.380 distance: 84 - 85: 7.493 distance: 85 - 86: 3.672 distance: 85 - 88: 5.363 distance: 86 - 87: 8.440 distance: 86 - 89: 8.140 distance: 87 - 114: 26.947 distance: 89 - 90: 11.990 distance: 90 - 91: 6.457 distance: 90 - 93: 11.331 distance: 91 - 92: 12.778 distance: 91 - 97: 18.832 distance: 93 - 94: 12.466 distance: 93 - 95: 10.716 distance: 94 - 96: 6.746 distance: 97 - 98: 7.307 distance: 98 - 99: 7.040 distance: 98 - 101: 9.679 distance: 99 - 100: 14.571 distance: 99 - 106: 13.495 distance: 101 - 102: 11.920 distance: 102 - 103: 9.682 distance: 103 - 104: 5.543 distance: 103 - 105: 8.766 distance: 106 - 107: 9.292 distance: 107 - 108: 7.140 distance: 107 - 110: 18.956 distance: 108 - 109: 20.933 distance: 108 - 114: 17.234 distance: 110 - 111: 13.944 distance: 111 - 112: 13.877 distance: 111 - 113: 19.825 distance: 114 - 115: 32.530 distance: 115 - 116: 7.987 distance: 116 - 117: 16.267 distance: 116 - 118: 39.990 distance: 118 - 119: 10.690 distance: 119 - 120: 7.695 distance: 119 - 122: 13.158 distance: 120 - 121: 20.580 distance: 120 - 127: 19.393 distance: 122 - 123: 10.614 distance: 123 - 124: 16.560 distance: 124 - 125: 13.087 distance: 124 - 126: 5.525