Starting phenix.real_space_refine on Sun Jun 8 19:38:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8brd_16212/06_2025/8brd_16212.cif Found real_map, /net/cci-nas-00/data/ceres_data/8brd_16212/06_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_16212/06_2025/8brd_16212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8brd_16212/06_2025/8brd_16212.map" model { file = "/net/cci-nas-00/data/ceres_data/8brd_16212/06_2025/8brd_16212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8brd_16212/06_2025/8brd_16212.cif" } resolution = 2.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.099 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.82, per 1000 atoms: 0.69 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: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.88 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: 2.72 Time building geometry restraints manager: 2.91 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: 5.020 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.790 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 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:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.740 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.008 0.002 TRP F 18 HIS 0.003 0.001 HIS A 136 PHE 0.049 0.002 PHE A 44 TYR 0.016 0.001 TYR E 188 ARG 0.011 0.001 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.10488 ( 880) hydrogen bonds : angle 5.34245 ( 2595) covalent geometry : bond 0.00474 (10060) covalent geometry : angle 0.83128 (13549) *********************** 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 : 0.988 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: 1.3722 time to fit residues: 334.6257 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 : 0.979 ------------------------------------------------------------------------------- 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 109 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 52 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4622 r_free = 0.4622 target = 0.241291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164939 restraints weight = 8853.881| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.97 r_work: 0.3750 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10060 Z= 0.144 Angle : 0.537 6.682 13549 Z= 0.280 Chirality : 0.038 0.137 1596 Planarity : 0.005 0.071 1729 Dihedral : 5.333 53.935 1402 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.89 % Allowed : 17.18 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.23), residues: 1298 helix: 2.05 (0.16), residues: 1102 sheet: None (None), residues: 0 loop : -0.28 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 18 HIS 0.001 0.001 HIS B 136 PHE 0.024 0.002 PHE A 44 TYR 0.006 0.001 TYR D 237 ARG 0.005 0.000 ARG C 208 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 880) hydrogen bonds : angle 4.27885 ( 2595) covalent geometry : bond 0.00320 (10060) covalent geometry : angle 0.53676 (13549) *********************** 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 242 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 191 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.2657 (OUTLIER) cc_final: 0.2403 (pp) REVERT: A 9 LEU cc_start: 0.3169 (OUTLIER) cc_final: 0.2482 (mt) REVERT: A 48 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.6828 (mpp) REVERT: A 52 MET cc_start: 0.7556 (mmt) cc_final: 0.7307 (mmm) REVERT: E 52 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7288 (tpt) REVERT: E 59 THR cc_start: 0.8307 (m) cc_final: 0.7945 (p) REVERT: E 83 MET cc_start: 0.4902 (mmm) cc_final: 0.4681 (ttm) REVERT: E 155 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8505 (tmm) REVERT: E 165 MET cc_start: 0.8418 (mtp) cc_final: 0.7975 (mtp) REVERT: E 173 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7730 (mmtt) REVERT: E 219 MET cc_start: 0.4901 (ttp) cc_final: 0.4199 (tpt) REVERT: D 48 MET cc_start: 0.7497 (mtp) cc_final: 0.7266 (mmm) REVERT: D 49 LYS cc_start: 0.8013 (mtpt) cc_final: 0.7767 (mttt) REVERT: D 67 MET cc_start: 0.8221 (ptp) cc_final: 0.7951 (mtm) REVERT: D 144 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8205 (ttm-80) REVERT: C 1 MET cc_start: 0.6283 (mmm) cc_final: 0.5967 (tpp) REVERT: C 64 LYS cc_start: 0.7050 (mmtm) cc_final: 0.6821 (mttm) REVERT: C 67 MET cc_start: 0.7178 (mtp) cc_final: 0.6166 (mmm) REVERT: C 126 LYS cc_start: 0.7694 (mmmt) cc_final: 0.7165 (mttp) REVERT: C 135 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7553 (mtm-85) REVERT: C 179 MET cc_start: 0.8342 (tpt) cc_final: 0.8130 (tpp) REVERT: C 186 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8361 (m) REVERT: C 203 LYS cc_start: 0.8278 (tppt) cc_final: 0.7997 (tptt) REVERT: C 208 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7111 (ttp-110) REVERT: C 211 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7352 (mm-30) REVERT: B 36 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.7838 (mp) REVERT: B 67 MET cc_start: 0.7191 (ptp) cc_final: 0.6943 (ptm) REVERT: B 71 ASP cc_start: 0.6587 (m-30) cc_final: 0.6211 (t70) REVERT: B 75 ASP cc_start: 0.7591 (m-30) cc_final: 0.7300 (m-30) REVERT: B 135 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7756 (ttm170) REVERT: B 173 LYS cc_start: 0.7538 (pttp) cc_final: 0.7175 (mmpt) REVERT: B 202 ASP cc_start: 0.7804 (m-30) cc_final: 0.7557 (m-30) REVERT: F 25 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8019 (tp) REVERT: G 30 MET cc_start: 0.8233 (ttp) cc_final: 0.7797 (tmm) REVERT: G 41 GLU cc_start: 0.7743 (tp30) cc_final: 0.7451 (tm-30) outliers start: 51 outliers final: 12 residues processed: 215 average time/residue: 1.2999 time to fit residues: 298.7104 Evaluate side-chains 202 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU 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 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 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 108 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4600 r_free = 0.4600 target = 0.239179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.162327 restraints weight = 8913.814| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.01 r_work: 0.3724 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10060 Z= 0.162 Angle : 0.543 7.772 13549 Z= 0.284 Chirality : 0.039 0.128 1596 Planarity : 0.005 0.055 1729 Dihedral : 4.701 53.729 1382 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.80 % Allowed : 17.18 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.23), residues: 1298 helix: 2.04 (0.15), residues: 1090 sheet: None (None), residues: 0 loop : -0.06 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 18 HIS 0.001 0.000 HIS C 116 PHE 0.017 0.002 PHE F 39 TYR 0.008 0.001 TYR D 237 ARG 0.007 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 880) hydrogen bonds : angle 4.23920 ( 2595) covalent geometry : bond 0.00377 (10060) covalent geometry : angle 0.54318 (13549) *********************** 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: 50 poor density : 183 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3046 (OUTLIER) cc_final: 0.2369 (mt) REVERT: A 18 MET cc_start: 0.2929 (tpt) cc_final: 0.2686 (tmm) REVERT: A 48 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.6734 (mpp) REVERT: A 52 MET cc_start: 0.7613 (mmt) cc_final: 0.7342 (mmm) REVERT: A 105 MET cc_start: 0.5867 (ttm) cc_final: 0.5656 (ttp) REVERT: E 52 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7156 (tpt) REVERT: E 59 THR cc_start: 0.8236 (m) cc_final: 0.7972 (p) REVERT: E 155 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8467 (tmm) REVERT: E 165 MET cc_start: 0.8473 (mtp) cc_final: 0.8037 (mtp) REVERT: E 173 LYS cc_start: 0.8389 (mmtt) cc_final: 0.7732 (mmtt) REVERT: E 219 MET cc_start: 0.4918 (ttp) cc_final: 0.4270 (tpt) REVERT: D 49 LYS cc_start: 0.8089 (mtpt) cc_final: 0.7792 (mttt) REVERT: D 67 MET cc_start: 0.8244 (ptp) cc_final: 0.7970 (mtm) REVERT: D 128 ASP cc_start: 0.6389 (OUTLIER) cc_final: 0.5871 (t0) REVERT: D 144 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.8226 (ttm-80) REVERT: C 1 MET cc_start: 0.6336 (mmm) cc_final: 0.6034 (tpp) REVERT: C 64 LYS cc_start: 0.7004 (mmtm) cc_final: 0.6753 (mttm) REVERT: C 67 MET cc_start: 0.7210 (mtp) cc_final: 0.6389 (mmp) REVERT: C 103 THR cc_start: 0.7103 (OUTLIER) cc_final: 0.6802 (m) REVERT: C 126 LYS cc_start: 0.7724 (mmmt) cc_final: 0.7163 (mttp) REVERT: C 135 ARG cc_start: 0.7959 (mtm-85) cc_final: 0.7698 (mtm-85) REVERT: C 179 MET cc_start: 0.8347 (tpt) cc_final: 0.8046 (tpp) REVERT: C 186 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8367 (m) REVERT: C 208 ARG cc_start: 0.8038 (ttp80) cc_final: 0.6936 (ttp-110) REVERT: B 36 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.7948 (mp) REVERT: B 67 MET cc_start: 0.7206 (ptp) cc_final: 0.6974 (ptm) REVERT: B 71 ASP cc_start: 0.6640 (m-30) cc_final: 0.6233 (t70) REVERT: B 75 ASP cc_start: 0.7519 (m-30) cc_final: 0.7227 (m-30) REVERT: B 98 MET cc_start: 0.3881 (ptt) cc_final: 0.2433 (pmt) REVERT: B 135 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7719 (ttm170) REVERT: B 148 ASP cc_start: 0.8409 (m-30) cc_final: 0.8053 (m-30) REVERT: B 173 LYS cc_start: 0.7573 (pttp) cc_final: 0.7171 (mmpt) REVERT: F 25 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7968 (tp) REVERT: F 41 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6865 (pt0) REVERT: F 46 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7835 (mtpt) REVERT: G 30 MET cc_start: 0.8246 (ttp) cc_final: 0.7854 (tmm) REVERT: G 41 GLU cc_start: 0.7897 (tp30) cc_final: 0.7654 (mm-30) outliers start: 50 outliers final: 15 residues processed: 203 average time/residue: 1.4355 time to fit residues: 309.7807 Evaluate side-chains 208 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 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 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 132 THR Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain G residue 24 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 16 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 125 optimal weight: 0.0050 chunk 89 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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** E 138 GLN E 214 ASN C 138 GLN B 168 ASN F 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.239291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.164067 restraints weight = 8814.375| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.29 r_work: 0.3724 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10060 Z= 0.141 Angle : 0.518 8.493 13549 Z= 0.267 Chirality : 0.037 0.122 1596 Planarity : 0.005 0.056 1729 Dihedral : 4.675 58.237 1382 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.61 % Allowed : 17.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.23), residues: 1298 helix: 2.17 (0.15), residues: 1090 sheet: None (None), residues: 0 loop : -0.04 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 18 HIS 0.001 0.000 HIS C 136 PHE 0.028 0.002 PHE A 44 TYR 0.006 0.001 TYR D 237 ARG 0.007 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 880) hydrogen bonds : angle 4.11680 ( 2595) covalent geometry : bond 0.00324 (10060) covalent geometry : angle 0.51775 (13549) *********************** 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 231 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3004 (OUTLIER) cc_final: 0.2337 (mt) REVERT: A 32 VAL cc_start: 0.7779 (OUTLIER) cc_final: 0.7426 (t) REVERT: A 48 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6642 (mpp) REVERT: A 52 MET cc_start: 0.7619 (mmt) cc_final: 0.7351 (mmm) REVERT: E 28 MET cc_start: 0.5302 (ptt) cc_final: 0.4945 (ptt) REVERT: E 52 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7168 (tpt) REVERT: E 59 THR cc_start: 0.8270 (m) cc_final: 0.8019 (p) REVERT: E 155 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8476 (tmm) REVERT: E 165 MET cc_start: 0.8459 (mtp) cc_final: 0.8011 (mtp) REVERT: E 173 LYS cc_start: 0.8415 (mmtt) cc_final: 0.7756 (mmtt) REVERT: E 219 MET cc_start: 0.4939 (ttp) cc_final: 0.4293 (tpt) REVERT: D 49 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7850 (mttt) REVERT: D 60 LYS cc_start: 0.6690 (OUTLIER) cc_final: 0.6466 (mttp) REVERT: D 67 MET cc_start: 0.8273 (ptp) cc_final: 0.8037 (mtm) REVERT: D 83 MET cc_start: 0.5906 (mpp) cc_final: 0.5558 (mpp) REVERT: D 144 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.8216 (ttm-80) REVERT: D 173 LYS cc_start: 0.8157 (mttt) cc_final: 0.7947 (mttm) REVERT: C 1 MET cc_start: 0.6336 (mmm) cc_final: 0.6049 (tpp) REVERT: C 64 LYS cc_start: 0.7019 (mmtm) cc_final: 0.6729 (mttm) REVERT: C 67 MET cc_start: 0.7162 (mtp) cc_final: 0.6349 (mmp) REVERT: C 135 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7737 (mtm-85) REVERT: C 179 MET cc_start: 0.8335 (tpt) cc_final: 0.8107 (tpp) REVERT: C 186 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8365 (m) REVERT: C 208 ARG cc_start: 0.8054 (ttp80) cc_final: 0.6914 (ttp-110) REVERT: B 36 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7989 (mp) REVERT: B 52 MET cc_start: 0.8018 (mmm) cc_final: 0.7708 (mmt) REVERT: B 67 MET cc_start: 0.7252 (ptp) cc_final: 0.7019 (ptm) REVERT: B 71 ASP cc_start: 0.6656 (m-30) cc_final: 0.6246 (t70) REVERT: B 75 ASP cc_start: 0.7567 (m-30) cc_final: 0.7276 (m-30) REVERT: B 83 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.6252 (mpp) REVERT: B 135 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7633 (ttm170) REVERT: B 148 ASP cc_start: 0.8423 (m-30) cc_final: 0.8070 (m-30) REVERT: B 155 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8142 (tpt) REVERT: B 168 ASN cc_start: 0.8283 (m-40) cc_final: 0.8066 (m110) REVERT: B 173 LYS cc_start: 0.7551 (pttp) cc_final: 0.7164 (mmpt) REVERT: F 25 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7974 (tp) REVERT: G 30 MET cc_start: 0.8285 (ttp) cc_final: 0.7837 (tmm) REVERT: G 41 GLU cc_start: 0.7881 (tp30) cc_final: 0.7667 (mm-30) outliers start: 48 outliers final: 16 residues processed: 202 average time/residue: 1.3786 time to fit residues: 297.0967 Evaluate side-chains 209 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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 61 ILE 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 20 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 137 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 155 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 56 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** 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 = 0.4594 r_free = 0.4594 target = 0.238400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.161671 restraints weight = 8788.689| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.14 r_work: 0.3721 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10060 Z= 0.151 Angle : 0.522 7.495 13549 Z= 0.271 Chirality : 0.037 0.125 1596 Planarity : 0.005 0.057 1729 Dihedral : 4.700 58.398 1382 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.32 % Allowed : 18.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.23), residues: 1298 helix: 2.18 (0.15), residues: 1089 sheet: None (None), residues: 0 loop : 0.02 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 18 HIS 0.002 0.000 HIS C 136 PHE 0.016 0.002 PHE F 39 TYR 0.006 0.001 TYR D 237 ARG 0.007 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 880) hydrogen bonds : angle 4.14046 ( 2595) covalent geometry : bond 0.00350 (10060) covalent geometry : angle 0.52224 (13549) *********************** 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 230 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3041 (OUTLIER) cc_final: 0.2390 (mt) REVERT: A 48 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6686 (mpp) REVERT: A 52 MET cc_start: 0.7682 (mmt) cc_final: 0.7441 (mmm) REVERT: A 64 LYS cc_start: 0.7068 (mttt) cc_final: 0.6705 (mtpt) REVERT: A 69 LYS cc_start: 0.6417 (tptp) cc_final: 0.5912 (mppt) REVERT: E 28 MET cc_start: 0.5282 (ptt) cc_final: 0.4898 (ptt) REVERT: E 52 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7282 (tpt) REVERT: E 59 THR cc_start: 0.8292 (m) cc_final: 0.8008 (p) REVERT: E 155 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8477 (tmm) REVERT: E 165 MET cc_start: 0.8458 (mtp) cc_final: 0.8126 (mtp) REVERT: E 173 LYS cc_start: 0.8471 (mmtt) cc_final: 0.7812 (mmtt) REVERT: E 219 MET cc_start: 0.4928 (ttp) cc_final: 0.4279 (tpt) REVERT: D 49 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7885 (mttt) REVERT: D 60 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6597 (mttp) REVERT: D 64 LYS cc_start: 0.7916 (ptpp) cc_final: 0.6676 (pptt) REVERT: D 67 MET cc_start: 0.8216 (ptp) cc_final: 0.7975 (mtm) REVERT: D 83 MET cc_start: 0.5898 (mpp) cc_final: 0.5481 (mpp) REVERT: D 128 ASP cc_start: 0.6392 (OUTLIER) cc_final: 0.6139 (m-30) REVERT: D 173 LYS cc_start: 0.8198 (mttt) cc_final: 0.7997 (mttp) REVERT: C 64 LYS cc_start: 0.7022 (mmtm) cc_final: 0.6740 (mttm) REVERT: C 103 THR cc_start: 0.7053 (OUTLIER) cc_final: 0.6828 (m) REVERT: C 134 GLU cc_start: 0.8112 (pt0) cc_final: 0.7745 (tt0) REVERT: C 135 ARG cc_start: 0.7970 (mtm-85) cc_final: 0.7739 (mtm-85) REVERT: C 179 MET cc_start: 0.8343 (tpt) cc_final: 0.8092 (tpp) REVERT: C 186 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8376 (m) REVERT: C 208 ARG cc_start: 0.8074 (ttp80) cc_final: 0.6953 (ttp-110) REVERT: B 36 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8073 (mp) REVERT: B 52 MET cc_start: 0.8043 (mmm) cc_final: 0.7740 (mmt) REVERT: B 67 MET cc_start: 0.7307 (ptp) cc_final: 0.7062 (ptm) REVERT: B 71 ASP cc_start: 0.6640 (m-30) cc_final: 0.6239 (t70) REVERT: B 75 ASP cc_start: 0.7554 (m-30) cc_final: 0.7260 (m-30) REVERT: B 135 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7711 (ttm170) REVERT: B 148 ASP cc_start: 0.8420 (m-30) cc_final: 0.8099 (m-30) REVERT: B 155 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8222 (tpt) REVERT: B 168 ASN cc_start: 0.8481 (m110) cc_final: 0.8258 (m110) REVERT: B 173 LYS cc_start: 0.7564 (pttp) cc_final: 0.7191 (mmpt) REVERT: F 25 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7993 (tp) REVERT: G 30 MET cc_start: 0.8287 (ttp) cc_final: 0.7853 (tmm) REVERT: G 41 GLU cc_start: 0.7881 (tp30) cc_final: 0.7678 (mm-30) outliers start: 45 outliers final: 19 residues processed: 208 average time/residue: 1.3794 time to fit residues: 305.7858 Evaluate side-chains 215 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 61 ILE 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 144 ARG 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 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 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 51 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 251 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 63 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 14 optimal weight: 0.0980 chunk 124 optimal weight: 0.0870 chunk 81 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.4609 r_free = 0.4609 target = 0.239969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.166105 restraints weight = 8890.985| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.25 r_work: 0.3740 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10060 Z= 0.123 Angle : 0.491 6.953 13549 Z= 0.256 Chirality : 0.036 0.118 1596 Planarity : 0.005 0.056 1729 Dihedral : 4.609 58.061 1382 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.22 % Allowed : 18.91 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.23), residues: 1298 helix: 2.37 (0.15), residues: 1092 sheet: None (None), residues: 0 loop : 0.04 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 18 HIS 0.001 0.000 HIS D 136 PHE 0.028 0.001 PHE A 44 TYR 0.006 0.001 TYR C 241 ARG 0.008 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 880) hydrogen bonds : angle 4.01897 ( 2595) covalent geometry : bond 0.00271 (10060) covalent geometry : angle 0.49111 (13549) *********************** 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 232 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3008 (OUTLIER) cc_final: 0.2336 (mt) REVERT: A 32 VAL cc_start: 0.7776 (OUTLIER) cc_final: 0.7417 (t) REVERT: A 48 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.6620 (mpp) REVERT: A 52 MET cc_start: 0.7657 (mmt) cc_final: 0.7423 (mmm) REVERT: A 64 LYS cc_start: 0.7016 (mttt) cc_final: 0.6627 (mtpt) REVERT: A 69 LYS cc_start: 0.6438 (tptp) cc_final: 0.5911 (mppt) REVERT: E 28 MET cc_start: 0.5085 (ptt) cc_final: 0.4781 (ptt) REVERT: E 52 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7273 (tpt) REVERT: E 59 THR cc_start: 0.8260 (m) cc_final: 0.7973 (p) REVERT: E 155 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8491 (tmm) REVERT: E 165 MET cc_start: 0.8443 (mtp) cc_final: 0.8052 (mtp) REVERT: E 173 LYS cc_start: 0.8466 (mmtt) cc_final: 0.7777 (mmtt) REVERT: E 219 MET cc_start: 0.4883 (ttp) cc_final: 0.4249 (tpt) REVERT: D 49 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7807 (mttt) REVERT: D 64 LYS cc_start: 0.7890 (ptpp) cc_final: 0.6590 (pptt) REVERT: D 67 MET cc_start: 0.8297 (ptp) cc_final: 0.8043 (mtm) REVERT: D 83 MET cc_start: 0.5813 (OUTLIER) cc_final: 0.5501 (mpp) REVERT: D 173 LYS cc_start: 0.8149 (mttt) cc_final: 0.7948 (mttp) REVERT: C 1 MET cc_start: 0.6266 (mmm) cc_final: 0.6034 (tpp) REVERT: C 64 LYS cc_start: 0.7003 (mmtm) cc_final: 0.6709 (mttm) REVERT: C 67 MET cc_start: 0.7349 (mtp) cc_final: 0.6366 (mmp) REVERT: C 135 ARG cc_start: 0.7959 (mtm-85) cc_final: 0.7735 (mtm-85) REVERT: C 179 MET cc_start: 0.8301 (tpt) cc_final: 0.8024 (tpp) REVERT: C 186 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8365 (m) REVERT: C 208 ARG cc_start: 0.8054 (ttp80) cc_final: 0.6996 (ttp-110) REVERT: B 36 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8071 (mp) REVERT: B 52 MET cc_start: 0.7967 (mmm) cc_final: 0.7665 (mmt) REVERT: B 67 MET cc_start: 0.7297 (ptp) cc_final: 0.7075 (ptm) REVERT: B 71 ASP cc_start: 0.6633 (m-30) cc_final: 0.6217 (t70) REVERT: B 75 ASP cc_start: 0.7565 (m-30) cc_final: 0.7265 (m-30) REVERT: B 148 ASP cc_start: 0.8434 (m-30) cc_final: 0.8069 (m-30) REVERT: B 168 ASN cc_start: 0.8552 (m110) cc_final: 0.8168 (m110) REVERT: B 173 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7160 (mmpt) REVERT: F 25 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7966 (tp) REVERT: G 30 MET cc_start: 0.8289 (ttp) cc_final: 0.7799 (tmm) REVERT: G 41 GLU cc_start: 0.7860 (tp30) cc_final: 0.7657 (mm-30) outliers start: 44 outliers final: 16 residues processed: 208 average time/residue: 1.5826 time to fit residues: 351.5874 Evaluate side-chains 214 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 61 ILE 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 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 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 7 optimal weight: 0.0040 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 121 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 ASN E 214 ASN C 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.240109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.165352 restraints weight = 8961.901| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.16 r_work: 0.3743 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10060 Z= 0.125 Angle : 0.498 6.859 13549 Z= 0.259 Chirality : 0.036 0.124 1596 Planarity : 0.004 0.054 1729 Dihedral : 4.586 57.886 1382 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.45 % Allowed : 19.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.23), residues: 1298 helix: 2.41 (0.15), residues: 1096 sheet: None (None), residues: 0 loop : -0.03 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 18 HIS 0.001 0.000 HIS D 136 PHE 0.015 0.001 PHE F 39 TYR 0.006 0.001 TYR C 241 ARG 0.008 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 880) hydrogen bonds : angle 4.00997 ( 2595) covalent geometry : bond 0.00278 (10060) covalent geometry : angle 0.49840 (13549) *********************** 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 223 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3009 (OUTLIER) cc_final: 0.2335 (mt) REVERT: A 32 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7433 (t) REVERT: A 48 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6643 (mpp) REVERT: A 52 MET cc_start: 0.7659 (mmt) cc_final: 0.7409 (mmm) REVERT: A 64 LYS cc_start: 0.7073 (mttt) cc_final: 0.6663 (mtpt) REVERT: A 69 LYS cc_start: 0.6451 (tptp) cc_final: 0.5933 (mppt) REVERT: E 28 MET cc_start: 0.5055 (ptt) cc_final: 0.4744 (ptt) REVERT: E 52 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7297 (tpt) REVERT: E 59 THR cc_start: 0.8276 (m) cc_final: 0.7996 (p) REVERT: E 155 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8515 (tmm) REVERT: E 165 MET cc_start: 0.8438 (mtp) cc_final: 0.8060 (mtp) REVERT: E 173 LYS cc_start: 0.8474 (mmtt) cc_final: 0.7808 (mmtt) REVERT: E 219 MET cc_start: 0.4893 (ttp) cc_final: 0.4247 (tpt) REVERT: D 49 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7866 (mttt) REVERT: D 64 LYS cc_start: 0.7881 (ptpp) cc_final: 0.6640 (pptt) REVERT: D 67 MET cc_start: 0.8277 (ptp) cc_final: 0.8016 (mtm) REVERT: D 83 MET cc_start: 0.5814 (OUTLIER) cc_final: 0.5466 (mpp) REVERT: C 1 MET cc_start: 0.6365 (mmm) cc_final: 0.6099 (tpp) REVERT: C 64 LYS cc_start: 0.7037 (mmtm) cc_final: 0.6757 (mttm) REVERT: C 67 MET cc_start: 0.7415 (mtp) cc_final: 0.6444 (mmp) REVERT: C 135 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7605 (mtm-85) REVERT: C 179 MET cc_start: 0.8311 (tpt) cc_final: 0.7992 (tpp) REVERT: C 186 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8373 (m) REVERT: C 208 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7036 (ttp-110) REVERT: B 36 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8084 (mp) REVERT: B 52 MET cc_start: 0.7992 (mmm) cc_final: 0.7707 (mmt) REVERT: B 67 MET cc_start: 0.7301 (ptp) cc_final: 0.7086 (ptm) REVERT: B 71 ASP cc_start: 0.6627 (m-30) cc_final: 0.6227 (t70) REVERT: B 75 ASP cc_start: 0.7585 (m-30) cc_final: 0.7277 (m-30) REVERT: B 148 ASP cc_start: 0.8430 (m-30) cc_final: 0.8076 (m-30) REVERT: B 168 ASN cc_start: 0.8598 (m110) cc_final: 0.8236 (m110) REVERT: B 173 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7183 (mmpt) REVERT: F 25 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7992 (tp) REVERT: F 55 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7264 (ttmt) REVERT: G 30 MET cc_start: 0.8279 (ttp) cc_final: 0.7793 (tmm) outliers start: 36 outliers final: 14 residues processed: 201 average time/residue: 1.4470 time to fit residues: 309.2468 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 : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 61 ILE 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 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 84 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 47 optimal weight: 0.0980 chunk 112 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.4610 r_free = 0.4610 target = 0.240191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.164457 restraints weight = 8937.475| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.05 r_work: 0.3737 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10060 Z= 0.124 Angle : 0.496 6.700 13549 Z= 0.258 Chirality : 0.036 0.123 1596 Planarity : 0.004 0.054 1729 Dihedral : 4.551 57.378 1382 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.45 % Allowed : 19.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.23), residues: 1298 helix: 2.39 (0.15), residues: 1104 sheet: None (None), residues: 0 loop : 0.10 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 18 HIS 0.001 0.000 HIS D 136 PHE 0.028 0.001 PHE A 44 TYR 0.005 0.001 TYR D 237 ARG 0.009 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 880) hydrogen bonds : angle 3.98952 ( 2595) covalent geometry : bond 0.00275 (10060) covalent geometry : angle 0.49605 (13549) *********************** 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 225 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.2893 (OUTLIER) cc_final: 0.2302 (mt) REVERT: A 32 VAL cc_start: 0.7751 (OUTLIER) cc_final: 0.7394 (t) REVERT: A 48 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6528 (mpp) REVERT: A 52 MET cc_start: 0.7646 (mmt) cc_final: 0.7416 (mmm) REVERT: A 64 LYS cc_start: 0.7012 (mttt) cc_final: 0.6588 (mtpt) REVERT: A 69 LYS cc_start: 0.6451 (tptp) cc_final: 0.5936 (mppt) REVERT: E 28 MET cc_start: 0.4915 (ptt) cc_final: 0.4629 (ptt) REVERT: E 52 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7448 (tpt) REVERT: E 59 THR cc_start: 0.8261 (m) cc_final: 0.7970 (p) REVERT: E 155 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8494 (tmm) REVERT: E 165 MET cc_start: 0.8436 (mtp) cc_final: 0.8084 (mtp) REVERT: E 173 LYS cc_start: 0.8484 (mmtt) cc_final: 0.7775 (mmtt) REVERT: E 219 MET cc_start: 0.4906 (ttp) cc_final: 0.4224 (tpt) REVERT: D 49 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7799 (mttt) REVERT: D 64 LYS cc_start: 0.7841 (ptpp) cc_final: 0.6592 (pptt) REVERT: D 67 MET cc_start: 0.8280 (ptp) cc_final: 0.8029 (mtm) REVERT: D 83 MET cc_start: 0.5797 (OUTLIER) cc_final: 0.5473 (mpp) REVERT: D 173 LYS cc_start: 0.8056 (mttt) cc_final: 0.7850 (mttp) REVERT: C 1 MET cc_start: 0.6321 (mmm) cc_final: 0.6050 (tpp) REVERT: C 64 LYS cc_start: 0.7037 (mmtm) cc_final: 0.6716 (mttm) REVERT: C 135 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7690 (mtm-85) REVERT: C 179 MET cc_start: 0.8291 (tpt) cc_final: 0.7959 (tpp) REVERT: C 186 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8350 (m) REVERT: C 208 ARG cc_start: 0.8054 (ttp80) cc_final: 0.6983 (ttp-110) REVERT: B 36 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8095 (mp) REVERT: B 52 MET cc_start: 0.7975 (mmm) cc_final: 0.7670 (mmt) REVERT: B 67 MET cc_start: 0.7313 (ptp) cc_final: 0.7095 (ptm) REVERT: B 71 ASP cc_start: 0.6612 (m-30) cc_final: 0.6192 (t70) REVERT: B 75 ASP cc_start: 0.7560 (m-30) cc_final: 0.7250 (m-30) REVERT: B 148 ASP cc_start: 0.8434 (m-30) cc_final: 0.8061 (m-30) REVERT: B 168 ASN cc_start: 0.8600 (m110) cc_final: 0.8213 (m110) REVERT: B 173 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7152 (mmpt) REVERT: F 25 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7950 (tp) REVERT: G 30 MET cc_start: 0.8284 (ttp) cc_final: 0.7784 (tmm) REVERT: G 41 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6242 (pm20) outliers start: 36 outliers final: 15 residues processed: 205 average time/residue: 1.3704 time to fit residues: 298.8157 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 : 0.969 ------------------------------------------------------------------------------- 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 61 ILE 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 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 113 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 ASN C 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.238465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.163391 restraints weight = 8881.437| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.08 r_work: 0.3711 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2671 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= 0.159 Angle : 0.547 10.043 13549 Z= 0.282 Chirality : 0.038 0.131 1596 Planarity : 0.005 0.057 1729 Dihedral : 4.637 53.696 1382 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.26 % Allowed : 19.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.23), residues: 1298 helix: 2.21 (0.15), residues: 1108 sheet: None (None), residues: 0 loop : -0.06 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 18 HIS 0.002 0.000 HIS D 136 PHE 0.018 0.002 PHE F 32 TYR 0.006 0.001 TYR D 237 ARG 0.008 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 880) hydrogen bonds : angle 4.15544 ( 2595) covalent geometry : bond 0.00372 (10060) covalent geometry : angle 0.54730 (13549) *********************** 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 218 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3083 (OUTLIER) cc_final: 0.2388 (mt) REVERT: A 32 VAL cc_start: 0.7740 (OUTLIER) cc_final: 0.7370 (t) REVERT: A 48 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.6585 (mpp) REVERT: A 52 MET cc_start: 0.7711 (mmt) cc_final: 0.7435 (mmm) REVERT: A 64 LYS cc_start: 0.7094 (mttt) cc_final: 0.6599 (mtpt) REVERT: A 69 LYS cc_start: 0.6605 (tptp) cc_final: 0.6131 (mppt) REVERT: E 28 MET cc_start: 0.5170 (ptt) cc_final: 0.4849 (ptt) REVERT: E 155 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8443 (tmm) REVERT: E 165 MET cc_start: 0.8464 (mtp) cc_final: 0.8129 (mtp) REVERT: E 173 LYS cc_start: 0.8492 (mmtt) cc_final: 0.7782 (mmtt) REVERT: E 219 MET cc_start: 0.4942 (ttp) cc_final: 0.4235 (tpt) REVERT: D 49 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7814 (mttt) REVERT: D 64 LYS cc_start: 0.7837 (ptpp) cc_final: 0.6618 (pptt) REVERT: D 83 MET cc_start: 0.5850 (OUTLIER) cc_final: 0.5462 (mpp) REVERT: D 128 ASP cc_start: 0.6266 (OUTLIER) cc_final: 0.6003 (m-30) REVERT: D 173 LYS cc_start: 0.8143 (mttt) cc_final: 0.7922 (mttp) REVERT: C 1 MET cc_start: 0.6340 (mmm) cc_final: 0.6063 (tpp) REVERT: C 64 LYS cc_start: 0.7020 (mmtm) cc_final: 0.6685 (mttm) REVERT: C 135 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7659 (mtm-85) REVERT: C 179 MET cc_start: 0.8331 (tpt) cc_final: 0.8041 (tpp) REVERT: C 186 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8375 (m) REVERT: C 208 ARG cc_start: 0.8022 (ttp80) cc_final: 0.6876 (ttp-110) REVERT: B 36 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8088 (mp) REVERT: B 52 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7648 (mmt) REVERT: B 67 MET cc_start: 0.7339 (ptp) cc_final: 0.7108 (ptm) REVERT: B 71 ASP cc_start: 0.6533 (m-30) cc_final: 0.6158 (t70) REVERT: B 75 ASP cc_start: 0.7575 (m-30) cc_final: 0.7269 (m-30) REVERT: B 148 ASP cc_start: 0.8478 (m-30) cc_final: 0.8240 (m-30) REVERT: B 168 ASN cc_start: 0.8519 (m110) cc_final: 0.8138 (m110) REVERT: B 173 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7176 (mmpt) REVERT: F 25 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7934 (tp) REVERT: G 30 MET cc_start: 0.8290 (ttp) cc_final: 0.7779 (tmm) REVERT: G 41 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7166 (tm-30) outliers start: 34 outliers final: 15 residues processed: 201 average time/residue: 1.7973 time to fit residues: 383.8694 Evaluate side-chains 210 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 2.773 ------------------------------------------------------------------------------- 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 61 ILE 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 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 52 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 34 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 GLN D 168 ASN C 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.236472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.157134 restraints weight = 8516.139| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.78 r_work: 0.3558 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10060 Z= 0.139 Angle : 0.529 8.725 13549 Z= 0.272 Chirality : 0.037 0.162 1596 Planarity : 0.005 0.057 1729 Dihedral : 4.582 53.923 1382 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.98 % Allowed : 20.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.23), residues: 1298 helix: 2.27 (0.15), residues: 1109 sheet: None (None), residues: 0 loop : 0.07 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 18 HIS 0.001 0.000 HIS D 136 PHE 0.033 0.002 PHE A 44 TYR 0.005 0.001 TYR D 237 ARG 0.008 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 880) hydrogen bonds : angle 4.07741 ( 2595) covalent geometry : bond 0.00317 (10060) covalent geometry : angle 0.52906 (13549) ********************** 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 209 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.2948 (OUTLIER) cc_final: 0.2338 (mt) REVERT: A 48 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6548 (mpp) REVERT: A 52 MET cc_start: 0.7701 (mmt) cc_final: 0.7402 (mmm) REVERT: E 28 MET cc_start: 0.4951 (ptt) cc_final: 0.4663 (ptt) REVERT: E 155 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8454 (tmm) REVERT: E 165 MET cc_start: 0.8480 (mtp) cc_final: 0.8054 (mtp) REVERT: E 173 LYS cc_start: 0.8400 (mmtt) cc_final: 0.7647 (mmtt) REVERT: E 219 MET cc_start: 0.4911 (ttp) cc_final: 0.4190 (tpt) REVERT: D 49 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7674 (mttt) REVERT: D 64 LYS cc_start: 0.7774 (ptpp) cc_final: 0.6504 (pptt) REVERT: D 83 MET cc_start: 0.5757 (OUTLIER) cc_final: 0.5386 (mpp) REVERT: D 128 ASP cc_start: 0.6138 (OUTLIER) cc_final: 0.5843 (m-30) REVERT: C 1 MET cc_start: 0.6276 (mmm) cc_final: 0.5985 (tpp) REVERT: C 64 LYS cc_start: 0.6969 (mmtm) cc_final: 0.6617 (mttm) REVERT: C 135 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7610 (mtm-85) REVERT: C 179 MET cc_start: 0.8280 (tpt) cc_final: 0.7931 (tpp) REVERT: C 186 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8361 (m) REVERT: C 208 ARG cc_start: 0.8014 (ttp80) cc_final: 0.6812 (ttp-110) REVERT: B 36 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7947 (mp) REVERT: B 52 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7660 (mmt) REVERT: B 67 MET cc_start: 0.7319 (ptp) cc_final: 0.7082 (ptm) REVERT: B 71 ASP cc_start: 0.6565 (m-30) cc_final: 0.6147 (t70) REVERT: B 75 ASP cc_start: 0.7485 (m-30) cc_final: 0.7165 (m-30) REVERT: B 168 ASN cc_start: 0.8604 (m110) cc_final: 0.8222 (m110) REVERT: B 173 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7102 (mmpt) REVERT: F 25 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7830 (tp) REVERT: F 41 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6764 (pt0) REVERT: G 30 MET cc_start: 0.8343 (ttp) cc_final: 0.7800 (tmm) REVERT: G 41 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7032 (tm-30) outliers start: 31 outliers final: 14 residues processed: 193 average time/residue: 1.3858 time to fit residues: 284.5900 Evaluate side-chains 205 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 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 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 52 MET 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 B residue 251 ILE 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 127 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 168 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 = 0.4531 r_free = 0.4531 target = 0.235568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.156130 restraints weight = 8571.456| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.53 r_work: 0.3578 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2790 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= 0.142 Angle : 0.539 9.046 13549 Z= 0.277 Chirality : 0.037 0.206 1596 Planarity : 0.005 0.057 1729 Dihedral : 4.601 54.416 1382 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.17 % Allowed : 19.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.23), residues: 1298 helix: 2.21 (0.15), residues: 1117 sheet: None (None), residues: 0 loop : 0.09 (0.47), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 18 HIS 0.001 0.000 HIS D 136 PHE 0.016 0.002 PHE B 29 TYR 0.005 0.001 TYR D 237 ARG 0.008 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 880) hydrogen bonds : angle 4.09180 ( 2595) covalent geometry : bond 0.00326 (10060) covalent geometry : angle 0.53888 (13549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11496.25 seconds wall clock time: 200 minutes 13.36 seconds (12013.36 seconds total)