Starting phenix.real_space_refine on Sat Aug 23 05:07:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8brd_16212/08_2025/8brd_16212.cif Found real_map, /net/cci-nas-00/data/ceres_data/8brd_16212/08_2025/8brd_16212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8brd_16212/08_2025/8brd_16212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8brd_16212/08_2025/8brd_16212.map" model { file = "/net/cci-nas-00/data/ceres_data/8brd_16212/08_2025/8brd_16212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8brd_16212/08_2025/8brd_16212.cif" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.099 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: 5 Type Number sf(0) Gaussians S 92 5.16 5 Na 2 4.78 5 C 6392 2.51 5 N 1625 2.21 5 O 1818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 9929 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1881 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 243} Chain: "E" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1762 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 226} 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: "C" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1889 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 244} Chain: "B" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1762 Classifications: {'peptide': 233} Modifications used: {'COO': 1} 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} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.37, per 1000 atoms: 0.24 Number of scatterers: 9929 At special positions: 0 Unit cell: (99.008, 110.656, 112.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 Na 2 11.00 O 1818 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: 0.72 Conformation dependent library (CDL) restraints added in 271.5 milliseconds Enol-peptide restraints added in 476.8 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: 60 helices and 1 sheets defined 88.6% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 Processing helix chain 'A' and resid 25 through 29 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: 3.929A pdb=" N ASP A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 167 Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 174 through 196 removed outlier: 4.091A pdb=" N THR A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.319A 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: 3.555A pdb=" N ILE A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 removed outlier: 3.872A pdb=" N GLU A 244 " --> pdb=" O TYR A 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 244' Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.625A 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: 3.724A 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: 3.625A pdb=" N SER E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR E 241 " --> pdb=" O TYR E 237 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU E 242 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN E 243 " --> pdb=" O LYS E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 250 removed outlier: 4.355A pdb=" N ARG E 247 " --> pdb=" O GLU E 244 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU E 249 " --> pdb=" O LYS E 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 23 Processing helix chain 'D' and resid 26 through 30 removed outlier: 3.606A 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 Processing helix chain 'D' and resid 92 through 98 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: 3.697A pdb=" N ASN D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 196 removed outlier: 4.051A pdb=" N THR D 185 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 4.261A 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 removed outlier: 3.582A pdb=" N ASN D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 24 Processing helix chain 'C' and resid 31 through 50 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: 3.768A pdb=" N GLU C 96 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.582A 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: 3.955A pdb=" N THR C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.274A 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 245 Processing helix chain 'C' and resid 247 through 251 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: 3.885A pdb=" N GLU B 96 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 4.048A 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: 3.544A pdb=" N GLY B 176 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix removed outlier: 3.532A pdb=" N THR B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 228 Processing helix chain 'B' and resid 230 through 240 Processing helix chain 'B' and resid 241 through 244 removed outlier: 3.917A 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 Processing helix chain 'F' and resid 16 through 39 removed outlier: 3.717A pdb=" N GLY F 20 " --> pdb=" O PRO F 16 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE F 39 " --> pdb=" O LEU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 58 removed outlier: 3.753A pdb=" N GLN F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 39 removed outlier: 3.922A 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 42 880 hydrogen bonds defined for protein. 2595 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: 1.54 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1689 1.30 - 1.43: 2252 1.43 - 1.56: 5935 1.56 - 1.69: 2 1.69 - 1.82: 182 Bond restraints: 10060 Sorted by residual: bond pdb=" CA ALA F 51 " pdb=" CB ALA F 51 " ideal model delta sigma weight residual 1.528 1.427 0.101 1.59e-02 3.96e+03 4.05e+01 bond pdb=" C MET A 169 " pdb=" O MET A 169 " ideal model delta sigma weight residual 1.234 1.309 -0.075 1.20e-02 6.94e+03 3.95e+01 bond pdb=" C LEU G 17 " pdb=" O LEU G 17 " ideal model delta sigma weight residual 1.236 1.166 0.069 1.32e-02 5.74e+03 2.77e+01 bond pdb=" C PRO A 172 " pdb=" O PRO A 172 " ideal model delta sigma weight residual 1.235 1.168 0.067 1.30e-02 5.92e+03 2.63e+01 bond pdb=" C ARG E 144 " pdb=" O ARG E 144 " ideal model delta sigma weight residual 1.236 1.172 0.065 1.26e-02 6.30e+03 2.62e+01 ... (remaining 10055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.18: 13501 5.18 - 10.37: 43 10.37 - 15.55: 2 15.55 - 20.74: 0 20.74 - 25.92: 3 Bond angle restraints: 13549 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 122.19 101.25 20.94 1.21e+00 6.83e-01 3.00e+02 angle pdb=" C ASP B 227 " pdb=" CA ASP B 227 " pdb=" CB ASP B 227 " ideal model delta sigma weight residual 110.92 136.84 -25.92 1.59e+00 3.96e-01 2.66e+02 angle pdb=" N GLY E 24 " pdb=" CA GLY E 24 " pdb=" C GLY E 24 " ideal model delta sigma weight residual 113.18 89.04 24.14 2.37e+00 1.78e-01 1.04e+02 angle pdb=" N PRO A 172 " pdb=" CA PRO A 172 " pdb=" CB PRO A 172 " ideal model delta sigma weight residual 103.25 94.91 8.34 1.05e+00 9.07e-01 6.31e+01 angle pdb=" C GLU D 99 " pdb=" CA GLU D 99 " pdb=" CB GLU D 99 " ideal model delta sigma weight residual 110.51 95.54 14.97 1.89e+00 2.80e-01 6.27e+01 ... (remaining 13544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 5270 17.64 - 35.28: 593 35.28 - 52.92: 152 52.92 - 70.56: 32 70.56 - 88.21: 13 Dihedral angle restraints: 6060 sinusoidal: 2378 harmonic: 3682 Sorted by residual: dihedral pdb=" C ASP B 227 " pdb=" N ASP B 227 " pdb=" CA ASP B 227 " pdb=" CB ASP B 227 " ideal model delta harmonic sigma weight residual -122.60 -166.02 43.42 0 2.50e+00 1.60e-01 3.02e+02 dihedral pdb=" N ASP B 227 " pdb=" C ASP B 227 " pdb=" CA ASP B 227 " pdb=" CB ASP B 227 " ideal model delta harmonic sigma weight residual 122.80 160.72 -37.92 0 2.50e+00 1.60e-01 2.30e+02 dihedral pdb=" CD ARG B 88 " pdb=" NE ARG B 88 " pdb=" CZ ARG B 88 " pdb=" NH1 ARG B 88 " ideal model delta sinusoidal sigma weight residual 0.00 -60.78 60.78 1 1.00e+01 1.00e-02 4.91e+01 ... (remaining 6057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.358: 1595 0.358 - 0.717: 0 0.717 - 1.075: 0 1.075 - 1.433: 0 1.433 - 1.792: 1 Chirality restraints: 1596 Sorted by residual: chirality pdb=" CA ASP B 227 " pdb=" N ASP B 227 " pdb=" C ASP B 227 " pdb=" CB ASP B 227 " both_signs ideal model delta sigma weight residual False 2.51 0.72 1.79 2.00e-01 2.50e+01 8.02e+01 chirality pdb=" CA GLU D 99 " pdb=" N GLU D 99 " pdb=" C GLU D 99 " pdb=" CB GLU D 99 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA LYS F 48 " pdb=" N LYS F 48 " pdb=" C LYS F 48 " pdb=" CB LYS F 48 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1593 not shown) Planarity restraints: 1729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE F 58 " 0.089 2.00e-02 2.50e+03 1.56e-01 2.44e+02 pdb=" C PHE F 58 " -0.271 2.00e-02 2.50e+03 pdb=" O PHE F 58 " 0.097 2.00e-02 2.50e+03 pdb=" N GLY F 59 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 88 " 0.945 9.50e-02 1.11e+02 4.23e-01 1.09e+02 pdb=" NE ARG B 88 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG B 88 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 88 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 88 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 232 " -0.760 9.50e-02 1.11e+02 3.41e-01 7.08e+01 pdb=" NE ARG A 232 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG A 232 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 232 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 232 " -0.025 2.00e-02 2.50e+03 ... (remaining 1726 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 25 2.37 - 3.00: 5306 3.00 - 3.63: 16305 3.63 - 4.27: 23493 4.27 - 4.90: 39199 Nonbonded interactions: 84328 Sorted by model distance: nonbonded pdb=" SD MET C 20 " pdb=" CB ILE C 26 " model vdw 1.733 3.830 nonbonded pdb=" O HOH F 101 " pdb=" O HOH F 102 " model vdw 1.939 3.040 nonbonded pdb=" SD MET C 20 " pdb=" CA ILE C 26 " model vdw 2.127 3.830 nonbonded pdb=" O SER D 167 " pdb=" CG LYS G 55 " model vdw 2.140 3.440 nonbonded pdb=" OD2 ASP G 24 " pdb="NA NA G 101 " model vdw 2.154 2.470 ... (remaining 84323 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' and resid 11 through 61) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.160 Find NCS groups from input model: 0.210 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:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 0.101 10060 Z= 0.270 Angle : 0.831 25.922 13549 Z= 0.501 Chirality : 0.061 1.792 1596 Planarity : 0.017 0.423 1729 Dihedral : 16.180 88.206 3698 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.88 % Allowed : 18.04 % Favored : 79.08 % 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: 2.09 (0.23), residues: 1298 helix: 1.77 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -0.63 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 247 TYR 0.016 0.001 TYR E 188 PHE 0.049 0.002 PHE A 44 TRP 0.008 0.002 TRP F 18 HIS 0.003 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00474 (10060) covalent geometry : angle 0.83128 (13549) hydrogen bonds : bond 0.10488 ( 880) hydrogen bonds : angle 5.34245 ( 2595) *********************** 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 244 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3275 (OUTLIER) cc_final: 0.2724 (mt) REVERT: A 52 MET cc_start: 0.6903 (mmt) cc_final: 0.6611 (mmm) REVERT: A 75 ASP cc_start: 0.5150 (OUTLIER) cc_final: 0.4937 (m-30) REVERT: A 132 THR cc_start: 0.6698 (OUTLIER) cc_final: 0.6374 (p) REVERT: A 148 ASP cc_start: 0.8531 (m-30) cc_final: 0.8251 (m-30) REVERT: A 153 MET cc_start: 0.8178 (mmm) cc_final: 0.7859 (mmm) REVERT: A 195 MET cc_start: 0.7943 (mtp) cc_final: 0.7659 (mmm) REVERT: E 36 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7737 (mt) REVERT: E 48 MET cc_start: 0.7558 (mmm) cc_final: 0.7214 (mmm) REVERT: E 83 MET cc_start: 0.4991 (mmm) cc_final: 0.4383 (ttm) REVERT: E 155 MET cc_start: 0.8610 (tmm) cc_final: 0.8286 (tmm) REVERT: E 165 MET cc_start: 0.8225 (mtp) cc_final: 0.7843 (mtp) REVERT: E 173 LYS cc_start: 0.7731 (mmtt) cc_final: 0.7206 (mmtt) REVERT: E 219 MET cc_start: 0.4573 (ttp) cc_final: 0.3936 (tpt) REVERT: D 49 LYS cc_start: 0.7650 (mtpt) cc_final: 0.7347 (mttt) REVERT: D 153 MET cc_start: 0.8338 (mmm) cc_final: 0.8114 (tpp) REVERT: D 173 LYS cc_start: 0.7505 (mttt) cc_final: 0.7116 (mttm) REVERT: C 1 MET cc_start: 0.6202 (mmm) cc_final: 0.5993 (tpp) REVERT: C 60 LYS cc_start: 0.7434 (mttm) cc_final: 0.6934 (mtpt) REVERT: C 64 LYS cc_start: 0.6600 (mmtm) cc_final: 0.6395 (mttm) REVERT: C 67 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.5974 (mmm) REVERT: C 126 LYS cc_start: 0.7103 (mmmt) cc_final: 0.6531 (mttp) REVERT: C 131 LEU cc_start: 0.6636 (tp) cc_final: 0.6360 (mm) REVERT: C 135 ARG cc_start: 0.7137 (mtm-85) cc_final: 0.6792 (mtm-85) REVERT: C 138 GLN cc_start: 0.7181 (tt0) cc_final: 0.6702 (mt0) REVERT: C 179 MET cc_start: 0.8033 (tpt) cc_final: 0.7761 (tpp) REVERT: C 203 LYS cc_start: 0.7991 (tppt) cc_final: 0.7784 (tptt) REVERT: C 208 ARG cc_start: 0.7529 (ttp80) cc_final: 0.6530 (ttp-110) REVERT: B 67 MET cc_start: 0.6871 (ptp) cc_final: 0.6600 (ptm) REVERT: B 71 ASP cc_start: 0.6218 (m-30) cc_final: 0.5784 (t70) REVERT: B 75 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.7077 (m-30) REVERT: B 85 ASP cc_start: 0.4831 (OUTLIER) cc_final: 0.4411 (m-30) REVERT: B 134 GLU cc_start: 0.6583 (tp30) cc_final: 0.6083 (pt0) REVERT: B 173 LYS cc_start: 0.6960 (pttp) cc_final: 0.6710 (mmpt) REVERT: B 232 ARG cc_start: 0.4470 (OUTLIER) cc_final: 0.4087 (mmp80) REVERT: F 44 VAL cc_start: 0.7780 (t) cc_final: 0.7462 (m) REVERT: F 46 LYS cc_start: 0.7645 (mtmt) cc_final: 0.7345 (mtmt) REVERT: G 30 MET cc_start: 0.8092 (ttp) cc_final: 0.7780 (tmm) REVERT: G 41 GLU cc_start: 0.6608 (tp30) cc_final: 0.5101 (pm20) outliers start: 30 outliers final: 9 residues processed: 229 average time/residue: 0.6901 time to fit residues: 167.7633 Evaluate side-chains 206 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 232 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.242452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.165708 restraints weight = 8934.056| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.01 r_work: 0.3759 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10060 Z= 0.133 Angle : 0.526 6.789 13549 Z= 0.274 Chirality : 0.037 0.137 1596 Planarity : 0.005 0.058 1729 Dihedral : 5.300 58.353 1402 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.89 % Allowed : 16.99 % Favored : 78.12 % 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: 2.63 (0.23), residues: 1298 helix: 2.10 (0.16), residues: 1102 sheet: None (None), residues: 0 loop : -0.26 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 208 TYR 0.005 0.001 TYR D 237 PHE 0.023 0.002 PHE A 44 TRP 0.007 0.002 TRP F 18 HIS 0.002 0.001 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00290 (10060) covalent geometry : angle 0.52572 (13549) hydrogen bonds : bond 0.03990 ( 880) hydrogen bonds : angle 4.19635 ( 2595) *********************** 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 244 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3197 (OUTLIER) cc_final: 0.2577 (mt) REVERT: A 48 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6786 (mpp) REVERT: A 52 MET cc_start: 0.7504 (mmt) cc_final: 0.7250 (mmm) REVERT: E 59 THR cc_start: 0.8250 (m) cc_final: 0.7945 (p) REVERT: E 67 MET cc_start: 0.7075 (ptp) cc_final: 0.6604 (ptt) REVERT: E 155 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8497 (tmm) REVERT: E 165 MET cc_start: 0.8391 (mtp) cc_final: 0.7956 (mtp) REVERT: E 173 LYS cc_start: 0.8320 (mmtt) cc_final: 0.7734 (mmtt) REVERT: E 219 MET cc_start: 0.4891 (ttp) cc_final: 0.4245 (tpt) REVERT: D 49 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7750 (mttt) REVERT: D 67 MET cc_start: 0.8232 (ptp) cc_final: 0.7963 (mtm) REVERT: D 144 ARG cc_start: 0.8426 (ttm-80) cc_final: 0.8177 (ttm-80) REVERT: C 1 MET cc_start: 0.6293 (mmm) cc_final: 0.5985 (tpp) REVERT: C 60 LYS cc_start: 0.7820 (mttm) cc_final: 0.7446 (mtpt) REVERT: C 64 LYS cc_start: 0.7061 (mmtm) cc_final: 0.6830 (mttm) REVERT: C 67 MET cc_start: 0.7155 (mtp) cc_final: 0.6287 (mmm) REVERT: C 126 LYS cc_start: 0.7706 (mmmt) cc_final: 0.7179 (mttp) REVERT: C 135 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7543 (mtm-85) REVERT: C 179 MET cc_start: 0.8318 (tpt) cc_final: 0.8102 (tpp) REVERT: C 186 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8352 (m) REVERT: C 203 LYS cc_start: 0.8275 (tppt) cc_final: 0.8026 (tptt) REVERT: C 208 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7109 (ttp-110) REVERT: C 211 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7351 (mm-30) REVERT: B 36 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.7922 (mp) REVERT: B 67 MET cc_start: 0.7211 (ptp) cc_final: 0.6974 (ptm) REVERT: B 71 ASP cc_start: 0.6540 (m-30) cc_final: 0.6136 (t70) REVERT: B 75 ASP cc_start: 0.7456 (m-30) cc_final: 0.7164 (m-30) REVERT: B 135 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7728 (ttm170) REVERT: B 173 LYS cc_start: 0.7536 (pttp) cc_final: 0.7151 (mmpt) REVERT: F 25 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8034 (tp) REVERT: G 30 MET cc_start: 0.8229 (ttp) cc_final: 0.7786 (tmm) REVERT: G 41 GLU cc_start: 0.7742 (tp30) cc_final: 0.7432 (tm-30) outliers start: 51 outliers final: 13 residues processed: 216 average time/residue: 0.6719 time to fit residues: 154.3147 Evaluate side-chains 203 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain E residue 144 ARG Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 24 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 113 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 120 optimal weight: 0.4980 chunk 46 optimal weight: 0.0020 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 ASN C 138 GLN B 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.238995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.156179 restraints weight = 8793.475| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.75 r_work: 0.3722 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10060 Z= 0.161 Angle : 0.541 7.394 13549 Z= 0.282 Chirality : 0.038 0.129 1596 Planarity : 0.005 0.054 1729 Dihedral : 4.650 50.673 1382 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.89 % Allowed : 17.27 % Favored : 77.83 % 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: 2.62 (0.23), residues: 1298 helix: 2.09 (0.15), residues: 1089 sheet: None (None), residues: 0 loop : -0.06 (0.44), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 135 TYR 0.007 0.001 TYR D 237 PHE 0.018 0.002 PHE A 143 TRP 0.008 0.002 TRP F 18 HIS 0.001 0.000 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00374 (10060) covalent geometry : angle 0.54055 (13549) hydrogen bonds : bond 0.04175 ( 880) hydrogen bonds : angle 4.23023 ( 2595) *********************** 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 233 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 182 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3106 (OUTLIER) cc_final: 0.2467 (mt) REVERT: A 48 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.6745 (mpp) REVERT: A 52 MET cc_start: 0.7627 (mmt) cc_final: 0.7371 (mmm) REVERT: E 52 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7107 (tpt) REVERT: E 59 THR cc_start: 0.8295 (m) cc_final: 0.8002 (p) REVERT: E 67 MET cc_start: 0.7296 (ptp) cc_final: 0.6830 (ptt) REVERT: E 155 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8479 (tmm) REVERT: E 165 MET cc_start: 0.8467 (mtp) cc_final: 0.8033 (mtp) REVERT: E 173 LYS cc_start: 0.8378 (mmtt) cc_final: 0.7739 (mmtt) REVERT: E 219 MET cc_start: 0.4906 (ttp) cc_final: 0.4277 (tpt) REVERT: D 49 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7791 (mttt) REVERT: D 60 LYS cc_start: 0.6781 (OUTLIER) cc_final: 0.6456 (mttp) REVERT: D 67 MET cc_start: 0.8237 (ptp) cc_final: 0.7975 (mtm) REVERT: D 83 MET cc_start: 0.5985 (mpp) cc_final: 0.5538 (mpp) REVERT: D 128 ASP cc_start: 0.6405 (OUTLIER) cc_final: 0.5897 (t0) REVERT: D 144 ARG cc_start: 0.8487 (ttm-80) cc_final: 0.8206 (ttm-80) REVERT: C 1 MET cc_start: 0.6357 (mmm) cc_final: 0.6085 (tpp) REVERT: C 64 LYS cc_start: 0.6984 (mmtm) cc_final: 0.6753 (mttm) REVERT: C 67 MET cc_start: 0.7216 (mtp) cc_final: 0.6387 (mmp) REVERT: C 103 THR cc_start: 0.7148 (OUTLIER) cc_final: 0.6838 (m) REVERT: C 126 LYS cc_start: 0.7738 (mmmt) cc_final: 0.7203 (mttp) REVERT: C 128 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.7064 (t70) REVERT: C 135 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7707 (mtm-85) REVERT: C 179 MET cc_start: 0.8348 (tpt) cc_final: 0.8060 (tpp) REVERT: C 186 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8362 (m) REVERT: C 208 ARG cc_start: 0.8016 (ttp80) cc_final: 0.6922 (ttp-110) REVERT: B 36 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.7983 (mp) REVERT: B 67 MET cc_start: 0.7200 (ptp) cc_final: 0.6959 (ptm) REVERT: B 71 ASP cc_start: 0.6639 (m-30) cc_final: 0.6239 (t70) REVERT: B 75 ASP cc_start: 0.7532 (m-30) cc_final: 0.7225 (m-30) REVERT: B 98 MET cc_start: 0.3862 (ptt) cc_final: 0.2318 (pmt) REVERT: B 135 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7673 (ttm170) REVERT: B 173 LYS cc_start: 0.7563 (pttp) cc_final: 0.7173 (mmpt) REVERT: F 25 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7967 (tp) REVERT: G 30 MET cc_start: 0.8255 (ttp) cc_final: 0.7821 (tmm) outliers start: 51 outliers final: 17 residues processed: 206 average time/residue: 0.6776 time to fit residues: 148.1526 Evaluate side-chains 212 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 144 ARG Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 61 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 96 optimal weight: 0.0370 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 125 optimal weight: 0.0030 chunk 113 optimal weight: 0.7980 chunk 91 optimal weight: 0.0970 chunk 87 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.3066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 GLN E 214 ASN C 138 GLN B 168 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.241729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.166680 restraints weight = 8963.623| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.08 r_work: 0.3777 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 10060 Z= 0.116 Angle : 0.479 8.523 13549 Z= 0.248 Chirality : 0.036 0.126 1596 Planarity : 0.004 0.051 1729 Dihedral : 4.469 49.569 1382 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.65 % Allowed : 18.71 % Favored : 77.64 % 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: 3.01 (0.23), residues: 1298 helix: 2.36 (0.15), residues: 1091 sheet: None (None), residues: 0 loop : -0.00 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 135 TYR 0.004 0.001 TYR D 237 PHE 0.027 0.001 PHE A 44 TRP 0.006 0.002 TRP F 18 HIS 0.001 0.000 HIS E 136 Details of bonding type rmsd covalent geometry : bond 0.00241 (10060) covalent geometry : angle 0.47944 (13549) hydrogen bonds : bond 0.03673 ( 880) hydrogen bonds : angle 3.97136 ( 2595) *********************** 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 226 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3119 (OUTLIER) cc_final: 0.2476 (mt) REVERT: A 32 VAL cc_start: 0.7644 (OUTLIER) cc_final: 0.7302 (t) REVERT: A 48 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6592 (mpp) REVERT: A 52 MET cc_start: 0.7581 (mmt) cc_final: 0.7301 (mmm) REVERT: A 207 ARG cc_start: 0.7570 (tpp80) cc_final: 0.7366 (tpt-90) REVERT: E 52 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7129 (tpt) REVERT: E 67 MET cc_start: 0.7329 (ptp) cc_final: 0.6862 (ptt) REVERT: E 155 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8484 (tmm) REVERT: E 165 MET cc_start: 0.8403 (mtp) cc_final: 0.8029 (mtp) REVERT: E 173 LYS cc_start: 0.8369 (mmtt) cc_final: 0.7691 (mmtt) REVERT: E 219 MET cc_start: 0.4882 (ttp) cc_final: 0.4216 (tpt) REVERT: D 20 MET cc_start: 0.6251 (OUTLIER) cc_final: 0.6013 (tpp) REVERT: D 49 LYS cc_start: 0.7987 (mtpt) cc_final: 0.7695 (mttt) REVERT: D 60 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6331 (mttp) REVERT: D 64 LYS cc_start: 0.7823 (ptpp) cc_final: 0.6542 (pptt) REVERT: D 67 MET cc_start: 0.8222 (ptp) cc_final: 0.8000 (mtm) REVERT: D 83 MET cc_start: 0.5890 (mpp) cc_final: 0.5405 (mpp) REVERT: D 144 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.8156 (ttm-80) REVERT: D 173 LYS cc_start: 0.8048 (mttt) cc_final: 0.7822 (mttm) REVERT: C 1 MET cc_start: 0.6370 (mmm) cc_final: 0.6090 (tpp) REVERT: C 64 LYS cc_start: 0.6921 (mmtm) cc_final: 0.6655 (mttm) REVERT: C 67 MET cc_start: 0.7160 (mtp) cc_final: 0.6329 (mmp) REVERT: C 126 LYS cc_start: 0.7635 (mmmt) cc_final: 0.7102 (mttp) REVERT: C 135 ARG cc_start: 0.7865 (mtm-85) cc_final: 0.7611 (mtm-85) REVERT: C 138 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7208 (mt0) REVERT: C 179 MET cc_start: 0.8276 (tpt) cc_final: 0.8021 (tpp) REVERT: C 186 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8340 (m) REVERT: C 208 ARG cc_start: 0.8054 (ttp80) cc_final: 0.6964 (ttp-110) REVERT: B 36 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7982 (mp) REVERT: B 52 MET cc_start: 0.7987 (mmm) cc_final: 0.7687 (mmt) REVERT: B 67 MET cc_start: 0.7193 (ptp) cc_final: 0.6981 (ptm) REVERT: B 71 ASP cc_start: 0.6644 (m-30) cc_final: 0.6228 (t70) REVERT: B 75 ASP cc_start: 0.7569 (m-30) cc_final: 0.7260 (m-30) REVERT: B 83 MET cc_start: 0.6496 (OUTLIER) cc_final: 0.5736 (mtp) REVERT: B 148 ASP cc_start: 0.8350 (m-30) cc_final: 0.7953 (m-30) REVERT: B 173 LYS cc_start: 0.7491 (pttp) cc_final: 0.7083 (mmpt) REVERT: F 25 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7957 (tp) REVERT: G 30 MET cc_start: 0.8227 (ttp) cc_final: 0.7755 (tmm) outliers start: 38 outliers final: 8 residues processed: 204 average time/residue: 0.6762 time to fit residues: 146.6793 Evaluate side-chains 206 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain D residue 20 MET Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 24 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 44 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.239275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.163500 restraints weight = 8834.100| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 2.22 r_work: 0.3717 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10060 Z= 0.153 Angle : 0.515 7.061 13549 Z= 0.269 Chirality : 0.038 0.132 1596 Planarity : 0.005 0.054 1729 Dihedral : 4.598 53.512 1382 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.32 % Allowed : 18.43 % Favored : 77.26 % 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: 2.91 (0.23), residues: 1298 helix: 2.28 (0.15), residues: 1089 sheet: None (None), residues: 0 loop : 0.07 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 135 TYR 0.006 0.001 TYR D 237 PHE 0.019 0.002 PHE E 29 TRP 0.007 0.002 TRP F 18 HIS 0.002 0.000 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00356 (10060) covalent geometry : angle 0.51545 (13549) hydrogen bonds : bond 0.03985 ( 880) hydrogen bonds : angle 4.11855 ( 2595) *********************** 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 232 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.2973 (OUTLIER) cc_final: 0.2314 (mt) REVERT: A 32 VAL cc_start: 0.7759 (OUTLIER) cc_final: 0.7390 (t) REVERT: A 48 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6668 (mpp) REVERT: A 52 MET cc_start: 0.7672 (mmt) cc_final: 0.7398 (mmm) REVERT: E 52 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7255 (tpt) REVERT: E 67 MET cc_start: 0.7403 (ptp) cc_final: 0.6931 (ptt) REVERT: E 155 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8487 (tmm) REVERT: E 165 MET cc_start: 0.8478 (mtp) cc_final: 0.8106 (mtp) REVERT: E 173 LYS cc_start: 0.8400 (mmtt) cc_final: 0.7723 (mmtt) REVERT: E 219 MET cc_start: 0.4919 (ttp) cc_final: 0.4209 (tpt) REVERT: D 49 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7777 (mttt) REVERT: D 60 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6403 (mttp) REVERT: D 64 LYS cc_start: 0.7861 (ptpp) cc_final: 0.6599 (pptt) REVERT: D 67 MET cc_start: 0.8242 (ptp) cc_final: 0.8024 (mtm) REVERT: D 83 MET cc_start: 0.5919 (mpp) cc_final: 0.5294 (mpp) REVERT: D 173 LYS cc_start: 0.8133 (mttt) cc_final: 0.7914 (mttp) REVERT: C 1 MET cc_start: 0.6343 (mmm) cc_final: 0.6080 (tpp) REVERT: C 64 LYS cc_start: 0.6955 (mmtm) cc_final: 0.6654 (mttm) REVERT: C 103 THR cc_start: 0.6949 (OUTLIER) cc_final: 0.6742 (m) REVERT: C 134 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: C 135 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7651 (mtm-85) REVERT: C 179 MET cc_start: 0.8321 (tpt) cc_final: 0.8079 (tpp) REVERT: C 186 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8361 (m) REVERT: C 208 ARG cc_start: 0.8061 (ttp80) cc_final: 0.6879 (ttp-110) REVERT: B 36 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8042 (mp) REVERT: B 52 MET cc_start: 0.8040 (mmm) cc_final: 0.7726 (mmt) REVERT: B 67 MET cc_start: 0.7214 (ptp) cc_final: 0.6977 (ptm) REVERT: B 71 ASP cc_start: 0.6661 (m-30) cc_final: 0.6249 (t70) REVERT: B 75 ASP cc_start: 0.7636 (m-30) cc_final: 0.7328 (m-30) REVERT: B 148 ASP cc_start: 0.8451 (m-30) cc_final: 0.8057 (m-30) REVERT: B 155 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8250 (tpt) REVERT: B 173 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7157 (mmpt) REVERT: F 25 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7948 (tp) REVERT: F 55 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7251 (ttmt) REVERT: G 30 MET cc_start: 0.8279 (ttp) cc_final: 0.7842 (tmm) REVERT: G 41 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7348 (tm-30) outliers start: 45 outliers final: 12 residues processed: 207 average time/residue: 0.6340 time to fit residues: 139.6395 Evaluate side-chains 212 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 61 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 81 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 98 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.239851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.164557 restraints weight = 8948.648| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.43 r_work: 0.3735 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10060 Z= 0.135 Angle : 0.496 6.919 13549 Z= 0.260 Chirality : 0.037 0.126 1596 Planarity : 0.005 0.054 1729 Dihedral : 4.597 57.215 1382 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.32 % Allowed : 18.23 % Favored : 77.45 % 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: 2.94 (0.23), residues: 1298 helix: 2.27 (0.15), residues: 1105 sheet: None (None), residues: 0 loop : 0.10 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 135 TYR 0.006 0.001 TYR D 237 PHE 0.031 0.002 PHE A 44 TRP 0.007 0.002 TRP F 18 HIS 0.002 0.000 HIS E 116 Details of bonding type rmsd covalent geometry : bond 0.00306 (10060) covalent geometry : angle 0.49598 (13549) hydrogen bonds : bond 0.03819 ( 880) hydrogen bonds : angle 4.03940 ( 2595) *********************** 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 230 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.2998 (OUTLIER) cc_final: 0.2292 (mt) REVERT: A 32 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7387 (t) REVERT: A 48 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6627 (mpp) REVERT: A 52 MET cc_start: 0.7679 (mmt) cc_final: 0.7428 (mmm) REVERT: E 52 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7248 (tpt) REVERT: E 67 MET cc_start: 0.7410 (ptp) cc_final: 0.6967 (ptt) REVERT: E 98 MET cc_start: 0.3784 (OUTLIER) cc_final: 0.3574 (pp-130) REVERT: E 155 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8484 (tmm) REVERT: E 165 MET cc_start: 0.8465 (mtp) cc_final: 0.8075 (mtp) REVERT: E 173 LYS cc_start: 0.8422 (mmtt) cc_final: 0.7732 (mmtt) REVERT: E 219 MET cc_start: 0.4864 (ttp) cc_final: 0.4181 (tpt) REVERT: D 49 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7764 (mttt) REVERT: D 60 LYS cc_start: 0.6795 (OUTLIER) cc_final: 0.6379 (mttp) REVERT: D 64 LYS cc_start: 0.7822 (ptpp) cc_final: 0.6544 (pptt) REVERT: D 67 MET cc_start: 0.8246 (ptp) cc_final: 0.8042 (mtm) REVERT: D 83 MET cc_start: 0.5890 (mpp) cc_final: 0.5364 (mpp) REVERT: C 1 MET cc_start: 0.6295 (mmm) cc_final: 0.6028 (tpp) REVERT: C 64 LYS cc_start: 0.6925 (mmtm) cc_final: 0.6620 (mttm) REVERT: C 67 MET cc_start: 0.7290 (mtp) cc_final: 0.6300 (mmp) REVERT: C 134 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: C 135 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7680 (mtm-85) REVERT: C 179 MET cc_start: 0.8303 (tpt) cc_final: 0.8033 (tpp) REVERT: C 186 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8358 (m) REVERT: C 208 ARG cc_start: 0.8023 (ttp80) cc_final: 0.6922 (ttp-110) REVERT: B 36 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8064 (mp) REVERT: B 52 MET cc_start: 0.8008 (mmm) cc_final: 0.7691 (mmt) REVERT: B 67 MET cc_start: 0.7263 (ptp) cc_final: 0.7031 (ptm) REVERT: B 71 ASP cc_start: 0.6621 (m-30) cc_final: 0.6211 (t70) REVERT: B 75 ASP cc_start: 0.7583 (m-30) cc_final: 0.7274 (m-30) REVERT: B 148 ASP cc_start: 0.8448 (m-30) cc_final: 0.8064 (m-30) REVERT: B 173 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7151 (mmpt) REVERT: F 25 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7922 (tp) REVERT: G 30 MET cc_start: 0.8273 (ttp) cc_final: 0.7837 (tmm) REVERT: G 41 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7317 (tm-30) outliers start: 45 outliers final: 14 residues processed: 201 average time/residue: 0.6401 time to fit residues: 136.7005 Evaluate side-chains 208 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 18 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 chunk 121 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 214 ASN C 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.240009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.164612 restraints weight = 8867.329| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.14 r_work: 0.3740 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10060 Z= 0.132 Angle : 0.496 6.945 13549 Z= 0.260 Chirality : 0.037 0.140 1596 Planarity : 0.005 0.055 1729 Dihedral : 4.599 59.715 1382 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.74 % Allowed : 18.71 % Favored : 77.54 % 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: 2.98 (0.23), residues: 1298 helix: 2.30 (0.15), residues: 1107 sheet: None (None), residues: 0 loop : 0.03 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 135 TYR 0.005 0.001 TYR D 237 PHE 0.021 0.001 PHE E 29 TRP 0.007 0.002 TRP F 18 HIS 0.001 0.000 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00297 (10060) covalent geometry : angle 0.49632 (13549) hydrogen bonds : bond 0.03795 ( 880) hydrogen bonds : angle 4.02669 ( 2595) *********************** 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 222 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.2983 (OUTLIER) cc_final: 0.2290 (mt) REVERT: A 32 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7401 (t) REVERT: A 48 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6680 (mpp) REVERT: A 52 MET cc_start: 0.7687 (mmt) cc_final: 0.7424 (mmm) REVERT: E 52 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7305 (tpt) REVERT: E 67 MET cc_start: 0.7477 (ptp) cc_final: 0.7025 (ptt) REVERT: E 155 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8485 (tmm) REVERT: E 165 MET cc_start: 0.8468 (mtp) cc_final: 0.8040 (mtp) REVERT: E 173 LYS cc_start: 0.8435 (mmtt) cc_final: 0.7736 (mmtt) REVERT: E 219 MET cc_start: 0.4900 (ttp) cc_final: 0.4214 (tpt) REVERT: D 49 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7796 (mttt) REVERT: D 60 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6461 (mttp) REVERT: D 64 LYS cc_start: 0.7788 (ptpp) cc_final: 0.6532 (pptt) REVERT: D 67 MET cc_start: 0.8272 (ptp) cc_final: 0.8038 (mtm) REVERT: D 83 MET cc_start: 0.5909 (OUTLIER) cc_final: 0.5299 (mpp) REVERT: C 1 MET cc_start: 0.6363 (mmm) cc_final: 0.6091 (tpp) REVERT: C 64 LYS cc_start: 0.7007 (mmtm) cc_final: 0.6699 (mttm) REVERT: C 67 MET cc_start: 0.7391 (mtp) cc_final: 0.6430 (mmp) REVERT: C 134 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: C 135 ARG cc_start: 0.7940 (mtm-85) cc_final: 0.7708 (mtm-85) REVERT: C 179 MET cc_start: 0.8304 (tpt) cc_final: 0.7993 (tpp) REVERT: C 186 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8365 (m) REVERT: C 208 ARG cc_start: 0.8036 (ttp80) cc_final: 0.6935 (ttp-110) REVERT: B 36 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8118 (mp) REVERT: B 52 MET cc_start: 0.7982 (mmm) cc_final: 0.7680 (mmt) REVERT: B 67 MET cc_start: 0.7300 (ptp) cc_final: 0.7072 (ptm) REVERT: B 71 ASP cc_start: 0.6546 (m-30) cc_final: 0.6164 (t70) REVERT: B 75 ASP cc_start: 0.7559 (m-30) cc_final: 0.7240 (m-30) REVERT: B 98 MET cc_start: 0.3482 (ptt) cc_final: 0.3235 (ptt) REVERT: B 148 ASP cc_start: 0.8472 (m-30) cc_final: 0.8094 (m-30) REVERT: B 173 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7173 (mmpt) REVERT: F 25 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7927 (tp) REVERT: G 30 MET cc_start: 0.8271 (ttp) cc_final: 0.7837 (tmm) REVERT: G 41 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7275 (tm-30) outliers start: 39 outliers final: 12 residues processed: 200 average time/residue: 0.6158 time to fit residues: 131.1231 Evaluate side-chains 207 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN B 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.239277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.165665 restraints weight = 8879.271| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.26 r_work: 0.3729 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10060 Z= 0.146 Angle : 0.531 9.456 13549 Z= 0.272 Chirality : 0.037 0.138 1596 Planarity : 0.005 0.056 1729 Dihedral : 4.602 57.158 1382 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.55 % Allowed : 19.10 % Favored : 77.35 % 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: 2.99 (0.23), residues: 1298 helix: 2.31 (0.15), residues: 1100 sheet: None (None), residues: 0 loop : 0.10 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 135 TYR 0.006 0.001 TYR D 237 PHE 0.028 0.002 PHE A 44 TRP 0.007 0.002 TRP F 18 HIS 0.002 0.000 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00338 (10060) covalent geometry : angle 0.53077 (13549) hydrogen bonds : bond 0.03870 ( 880) hydrogen bonds : angle 4.07080 ( 2595) *********************** 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 222 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3081 (OUTLIER) cc_final: 0.2385 (mt) REVERT: A 18 MET cc_start: 0.3072 (tpt) cc_final: 0.2404 (tpt) REVERT: A 32 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7405 (t) REVERT: A 48 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6607 (mpp) REVERT: A 52 MET cc_start: 0.7693 (mmt) cc_final: 0.7400 (mmm) REVERT: A 64 LYS cc_start: 0.7081 (mttt) cc_final: 0.6647 (mtmt) REVERT: A 69 LYS cc_start: 0.6463 (tptp) cc_final: 0.5946 (mppt) REVERT: E 52 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7443 (tpt) REVERT: E 67 MET cc_start: 0.7518 (ptp) cc_final: 0.7083 (ptt) REVERT: E 155 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8469 (tmm) REVERT: E 165 MET cc_start: 0.8459 (mtp) cc_final: 0.8131 (mtp) REVERT: E 173 LYS cc_start: 0.8492 (mmtt) cc_final: 0.7802 (mmtt) REVERT: E 219 MET cc_start: 0.4922 (ttp) cc_final: 0.4202 (tpt) REVERT: D 49 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7862 (mttt) REVERT: D 64 LYS cc_start: 0.7888 (ptpp) cc_final: 0.6634 (pptt) REVERT: D 83 MET cc_start: 0.5939 (OUTLIER) cc_final: 0.5392 (mpp) REVERT: D 128 ASP cc_start: 0.6377 (OUTLIER) cc_final: 0.6109 (m-30) REVERT: C 1 MET cc_start: 0.6401 (mmm) cc_final: 0.6086 (tpp) REVERT: C 64 LYS cc_start: 0.7050 (mmtm) cc_final: 0.6748 (mttm) REVERT: C 67 MET cc_start: 0.7444 (mtp) cc_final: 0.6469 (mmp) REVERT: C 135 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7706 (mtm-85) REVERT: C 179 MET cc_start: 0.8331 (tpt) cc_final: 0.8030 (tpp) REVERT: C 186 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8380 (m) REVERT: C 208 ARG cc_start: 0.8052 (ttp80) cc_final: 0.6994 (ttp-110) REVERT: B 36 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8100 (mp) REVERT: B 52 MET cc_start: 0.7997 (mmm) cc_final: 0.7695 (mmt) REVERT: B 67 MET cc_start: 0.7312 (ptp) cc_final: 0.7087 (ptm) REVERT: B 71 ASP cc_start: 0.6556 (m-30) cc_final: 0.6179 (t70) REVERT: B 75 ASP cc_start: 0.7584 (m-30) cc_final: 0.7269 (m-30) REVERT: B 173 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7176 (mmpt) REVERT: F 25 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7958 (tp) REVERT: G 30 MET cc_start: 0.8274 (ttp) cc_final: 0.7778 (tmm) REVERT: G 41 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7283 (tm-30) outliers start: 37 outliers final: 14 residues processed: 199 average time/residue: 0.6378 time to fit residues: 134.5150 Evaluate side-chains 210 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 61 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 62 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 0.0170 chunk 121 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.239869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.165695 restraints weight = 8801.674| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.18 r_work: 0.3733 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10060 Z= 0.132 Angle : 0.512 8.493 13549 Z= 0.264 Chirality : 0.037 0.129 1596 Planarity : 0.005 0.056 1729 Dihedral : 4.544 56.406 1382 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.07 % Allowed : 19.96 % Favored : 76.97 % 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: 3.09 (0.23), residues: 1298 helix: 2.39 (0.15), residues: 1099 sheet: None (None), residues: 0 loop : 0.11 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 135 TYR 0.005 0.001 TYR E 241 PHE 0.017 0.001 PHE E 29 TRP 0.007 0.002 TRP F 18 HIS 0.001 0.000 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00299 (10060) covalent geometry : angle 0.51184 (13549) hydrogen bonds : bond 0.03738 ( 880) hydrogen bonds : angle 4.01037 ( 2595) *********************** 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 216 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.2906 (OUTLIER) cc_final: 0.2304 (mt) REVERT: A 32 VAL cc_start: 0.7754 (OUTLIER) cc_final: 0.7402 (t) REVERT: A 48 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6646 (mpp) REVERT: A 52 MET cc_start: 0.7698 (mmt) cc_final: 0.7430 (mmm) REVERT: A 64 LYS cc_start: 0.7081 (mttt) cc_final: 0.6636 (mtmt) REVERT: A 69 LYS cc_start: 0.6443 (tptp) cc_final: 0.5975 (mppt) REVERT: E 67 MET cc_start: 0.7521 (ptp) cc_final: 0.7078 (ptt) REVERT: E 155 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8461 (tmm) REVERT: E 165 MET cc_start: 0.8463 (mtp) cc_final: 0.8074 (mtp) REVERT: E 173 LYS cc_start: 0.8487 (mmtt) cc_final: 0.7783 (mmtt) REVERT: E 219 MET cc_start: 0.4906 (ttp) cc_final: 0.4199 (tpt) REVERT: D 49 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7832 (mttt) REVERT: D 64 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.6951 (ttpp) REVERT: D 83 MET cc_start: 0.5941 (OUTLIER) cc_final: 0.5371 (mpp) REVERT: C 1 MET cc_start: 0.6411 (mmm) cc_final: 0.6102 (tpp) REVERT: C 64 LYS cc_start: 0.7038 (mmtm) cc_final: 0.6726 (mttm) REVERT: C 135 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7677 (mtm-85) REVERT: C 179 MET cc_start: 0.8314 (tpt) cc_final: 0.7999 (tpp) REVERT: C 186 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8376 (m) REVERT: C 208 ARG cc_start: 0.8048 (ttp80) cc_final: 0.6962 (ttp-110) REVERT: B 36 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8111 (mp) REVERT: B 52 MET cc_start: 0.8002 (mmm) cc_final: 0.7700 (mmt) REVERT: B 67 MET cc_start: 0.7324 (ptp) cc_final: 0.7106 (ptm) REVERT: B 71 ASP cc_start: 0.6634 (m-30) cc_final: 0.6232 (t70) REVERT: B 75 ASP cc_start: 0.7586 (m-30) cc_final: 0.7273 (m-30) REVERT: B 173 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7200 (mmpt) REVERT: F 25 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7941 (tp) REVERT: F 41 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6788 (pt0) REVERT: G 30 MET cc_start: 0.8301 (ttp) cc_final: 0.7798 (tmm) REVERT: G 41 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7197 (tm-30) outliers start: 32 outliers final: 14 residues processed: 199 average time/residue: 0.6375 time to fit residues: 134.9412 Evaluate side-chains 210 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 64 LYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 61 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 94 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.236891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.156082 restraints weight = 8371.684| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.72 r_work: 0.3580 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10060 Z= 0.131 Angle : 0.519 8.765 13549 Z= 0.266 Chirality : 0.037 0.171 1596 Planarity : 0.005 0.056 1729 Dihedral : 4.528 56.231 1382 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.88 % Allowed : 20.15 % Favored : 76.97 % 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: 3.12 (0.23), residues: 1298 helix: 2.39 (0.15), residues: 1102 sheet: None (None), residues: 0 loop : 0.22 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 135 TYR 0.005 0.001 TYR D 237 PHE 0.036 0.002 PHE A 44 TRP 0.007 0.002 TRP F 18 HIS 0.001 0.000 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00296 (10060) covalent geometry : angle 0.51910 (13549) hydrogen bonds : bond 0.03731 ( 880) hydrogen bonds : angle 4.00042 ( 2595) ********************** REFINEMENT MACRO_CYCLE 10 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 215 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.2866 (OUTLIER) cc_final: 0.2257 (mt) REVERT: A 32 VAL cc_start: 0.7623 (OUTLIER) cc_final: 0.7219 (t) REVERT: A 48 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6628 (mpp) REVERT: A 52 MET cc_start: 0.7644 (mmt) cc_final: 0.7341 (mmm) REVERT: A 69 LYS cc_start: 0.6412 (tptp) cc_final: 0.5926 (mppt) REVERT: E 64 LYS cc_start: 0.7326 (mttm) cc_final: 0.6640 (tmtt) REVERT: E 67 MET cc_start: 0.7493 (ptp) cc_final: 0.7047 (ptt) REVERT: E 83 MET cc_start: 0.4885 (ttm) cc_final: 0.4487 (tpp) REVERT: E 155 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8485 (tmm) REVERT: E 165 MET cc_start: 0.8472 (mtp) cc_final: 0.8077 (mtp) REVERT: E 173 LYS cc_start: 0.8418 (mmtt) cc_final: 0.7676 (mmtt) REVERT: E 219 MET cc_start: 0.4905 (ttp) cc_final: 0.4185 (tpt) REVERT: D 49 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7705 (mttt) REVERT: D 64 LYS cc_start: 0.7802 (ptpp) cc_final: 0.6861 (ttpp) REVERT: D 83 MET cc_start: 0.5915 (OUTLIER) cc_final: 0.5331 (mpp) REVERT: D 128 ASP cc_start: 0.6092 (OUTLIER) cc_final: 0.5814 (m-30) REVERT: C 1 MET cc_start: 0.6305 (mmm) cc_final: 0.5957 (tpp) REVERT: C 64 LYS cc_start: 0.6970 (mmtm) cc_final: 0.6645 (mttm) REVERT: C 135 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7631 (mtm-85) REVERT: C 179 MET cc_start: 0.8277 (tpt) cc_final: 0.7929 (tpp) REVERT: C 186 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8357 (m) REVERT: C 208 ARG cc_start: 0.8054 (ttp80) cc_final: 0.6942 (ttp-110) REVERT: B 36 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8039 (mp) REVERT: B 52 MET cc_start: 0.7998 (mmm) cc_final: 0.7678 (mmt) REVERT: B 67 MET cc_start: 0.7308 (ptp) cc_final: 0.7083 (ptm) REVERT: B 71 ASP cc_start: 0.6647 (m-30) cc_final: 0.6202 (t70) REVERT: B 75 ASP cc_start: 0.7502 (m-30) cc_final: 0.7180 (m-30) REVERT: B 173 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7126 (mmpt) REVERT: F 25 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7841 (tp) REVERT: F 41 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6677 (pt0) REVERT: G 30 MET cc_start: 0.8312 (ttp) cc_final: 0.7765 (tmm) REVERT: G 41 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7042 (tm-30) outliers start: 30 outliers final: 11 residues processed: 198 average time/residue: 0.6137 time to fit residues: 128.8951 Evaluate side-chains 206 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 41 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 37 optimal weight: 0.8980 chunk 89 optimal weight: 0.0570 chunk 25 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 79 optimal weight: 0.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN C 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.236402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.161837 restraints weight = 8566.025| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.66 r_work: 0.3570 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10060 Z= 0.126 Angle : 0.514 8.541 13549 Z= 0.264 Chirality : 0.037 0.173 1596 Planarity : 0.004 0.055 1729 Dihedral : 4.498 56.496 1382 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.59 % Allowed : 20.35 % Favored : 77.06 % 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: 3.14 (0.23), residues: 1298 helix: 2.37 (0.15), residues: 1111 sheet: None (None), residues: 0 loop : 0.30 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 135 TYR 0.005 0.001 TYR E 241 PHE 0.018 0.001 PHE E 29 TRP 0.006 0.002 TRP F 18 HIS 0.001 0.000 HIS D 136 Details of bonding type rmsd covalent geometry : bond 0.00279 (10060) covalent geometry : angle 0.51434 (13549) hydrogen bonds : bond 0.03675 ( 880) hydrogen bonds : angle 3.97857 ( 2595) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5537.88 seconds wall clock time: 94 minutes 43.28 seconds (5683.28 seconds total)