Starting phenix.real_space_refine on Fri Nov 15 23:36:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brd_16212/11_2024/8brd_16212.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brd_16212/11_2024/8brd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brd_16212/11_2024/8brd_16212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brd_16212/11_2024/8brd_16212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brd_16212/11_2024/8brd_16212.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brd_16212/11_2024/8brd_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 7.99, per 1000 atoms: 0.80 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: 2.70 Conformation dependent library (CDL) restraints added in 1.2 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: 0.85 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: 2.87 Time building geometry restraints manager: 3.07 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: 0.010 Normalize map: mean=0, sd=1: 3.530 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.390 Find NCS groups from input model: 0.510 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.670 ------------------------------------------------------------------------------- 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= 0.314 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 *********************** 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 : 1.076 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: 1.4168 time to fit residues: 344.9471 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1367 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= 0.207 Angle : 0.537 6.683 13549 Z= 0.280 Chirality : 0.038 0.137 1596 Planarity : 0.005 0.071 1729 Dihedral : 5.333 53.888 1402 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.29 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: 2.56 (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 *********************** 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 : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.2674 (OUTLIER) cc_final: 0.2382 (pp) REVERT: A 9 LEU cc_start: 0.3134 (OUTLIER) cc_final: 0.2402 (mt) REVERT: A 48 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6684 (mpp) REVERT: A 52 MET cc_start: 0.7106 (mmt) cc_final: 0.6845 (mmm) REVERT: A 153 MET cc_start: 0.8283 (mmm) cc_final: 0.7912 (tpp) REVERT: A 195 MET cc_start: 0.8006 (mtp) cc_final: 0.7765 (mmm) REVERT: E 36 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7748 (mt) REVERT: E 52 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6855 (tpt) REVERT: E 59 THR cc_start: 0.7987 (m) cc_final: 0.7520 (p) REVERT: E 67 MET cc_start: 0.6831 (ptp) cc_final: 0.6309 (ptt) REVERT: E 83 MET cc_start: 0.4901 (mmm) cc_final: 0.4662 (ttm) REVERT: E 155 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8293 (tmm) REVERT: E 165 MET cc_start: 0.8366 (mtp) cc_final: 0.7917 (mtp) REVERT: E 173 LYS cc_start: 0.7800 (mmtt) cc_final: 0.7204 (mmtt) REVERT: E 219 MET cc_start: 0.4658 (ttp) cc_final: 0.3976 (tpt) REVERT: D 48 MET cc_start: 0.7270 (mtp) cc_final: 0.6973 (mmm) REVERT: D 49 LYS cc_start: 0.7610 (mtpt) cc_final: 0.7242 (mttt) REVERT: D 67 MET cc_start: 0.7941 (ptp) cc_final: 0.7656 (mtm) REVERT: D 144 ARG cc_start: 0.8070 (ttm-80) cc_final: 0.7808 (ttm-80) REVERT: C 1 MET cc_start: 0.6223 (mmm) cc_final: 0.5918 (tpp) REVERT: C 64 LYS cc_start: 0.6581 (mmtm) cc_final: 0.6353 (mttm) REVERT: C 67 MET cc_start: 0.6751 (mtp) cc_final: 0.5746 (mmm) REVERT: C 72 GLU cc_start: 0.7270 (tp30) cc_final: 0.7034 (tp30) REVERT: C 126 LYS cc_start: 0.7150 (mmmt) cc_final: 0.6574 (mttp) REVERT: C 131 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6460 (mm) REVERT: C 135 ARG cc_start: 0.7318 (mtm-85) cc_final: 0.6890 (mtm-85) REVERT: C 179 MET cc_start: 0.8082 (tpt) cc_final: 0.7802 (tpp) REVERT: C 186 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8333 (m) REVERT: C 203 LYS cc_start: 0.8081 (tppt) cc_final: 0.7799 (tptt) REVERT: C 208 ARG cc_start: 0.7595 (ttp80) cc_final: 0.6572 (ttp-110) REVERT: C 211 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6743 (mm-30) REVERT: B 36 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7612 (mp) REVERT: B 67 MET cc_start: 0.6918 (ptp) cc_final: 0.6652 (ptm) REVERT: B 71 ASP cc_start: 0.6345 (m-30) cc_final: 0.5903 (t70) REVERT: B 75 ASP cc_start: 0.7239 (m-30) cc_final: 0.6964 (m-30) REVERT: B 135 ARG cc_start: 0.7607 (ttm-80) cc_final: 0.7341 (ttm170) REVERT: B 173 LYS cc_start: 0.7053 (pttp) cc_final: 0.6669 (mmpt) REVERT: B 202 ASP cc_start: 0.7606 (m-30) cc_final: 0.7384 (m-30) REVERT: F 25 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7955 (tp) REVERT: F 46 LYS cc_start: 0.7793 (mtmt) cc_final: 0.7571 (mtpp) REVERT: G 30 MET cc_start: 0.8190 (ttp) cc_final: 0.7710 (tmm) REVERT: G 41 GLU cc_start: 0.6930 (tp30) cc_final: 0.6535 (tm-30) outliers start: 51 outliers final: 12 residues processed: 215 average time/residue: 1.3303 time to fit residues: 304.8843 Evaluate side-chains 205 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 36 LEU 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 131 LEU 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 65 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10060 Z= 0.240 Angle : 0.535 7.395 13549 Z= 0.279 Chirality : 0.038 0.127 1596 Planarity : 0.005 0.055 1729 Dihedral : 4.812 50.173 1384 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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: 2.01 (0.15), residues: 1097 sheet: None (None), residues: 0 loop : 0.00 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 18 HIS 0.001 0.000 HIS E 136 PHE 0.017 0.002 PHE F 39 TYR 0.007 0.001 TYR D 237 ARG 0.006 0.000 ARG A 135 *********************** 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 236 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3020 (OUTLIER) cc_final: 0.2363 (mt) REVERT: A 18 MET cc_start: 0.3001 (tpt) cc_final: 0.2778 (tmm) REVERT: A 48 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.6649 (mpp) REVERT: A 52 MET cc_start: 0.7178 (mmt) cc_final: 0.6912 (mmm) REVERT: A 195 MET cc_start: 0.8117 (mtp) cc_final: 0.7846 (mmm) REVERT: E 36 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7714 (mt) REVERT: E 52 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6717 (tpt) REVERT: E 59 THR cc_start: 0.7933 (m) cc_final: 0.7542 (p) REVERT: E 67 MET cc_start: 0.6939 (ptp) cc_final: 0.6418 (ptt) REVERT: E 83 MET cc_start: 0.4908 (mmm) cc_final: 0.4676 (mtp) REVERT: E 155 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8265 (tmm) REVERT: E 165 MET cc_start: 0.8430 (mtp) cc_final: 0.7995 (mtp) REVERT: E 173 LYS cc_start: 0.7857 (mmtt) cc_final: 0.7182 (mmtt) REVERT: E 219 MET cc_start: 0.4676 (ttp) cc_final: 0.4051 (tpt) REVERT: D 48 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.7082 (mmm) REVERT: D 49 LYS cc_start: 0.7636 (mtpt) cc_final: 0.7231 (mttt) REVERT: D 67 MET cc_start: 0.7961 (ptp) cc_final: 0.7718 (mtm) REVERT: D 83 MET cc_start: 0.5791 (mpp) cc_final: 0.5378 (mpp) REVERT: D 128 ASP cc_start: 0.5826 (OUTLIER) cc_final: 0.5397 (t0) REVERT: D 144 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7847 (ttm-80) REVERT: C 1 MET cc_start: 0.6206 (mmm) cc_final: 0.5915 (tpp) REVERT: C 64 LYS cc_start: 0.6530 (mmtm) cc_final: 0.6282 (mttm) REVERT: C 67 MET cc_start: 0.6816 (mtp) cc_final: 0.6038 (mmp) REVERT: C 72 GLU cc_start: 0.7330 (tp30) cc_final: 0.7109 (tp30) REVERT: C 103 THR cc_start: 0.6566 (OUTLIER) cc_final: 0.6314 (m) REVERT: C 126 LYS cc_start: 0.7149 (mmmt) cc_final: 0.6557 (mttp) REVERT: C 131 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6436 (mm) REVERT: C 135 ARG cc_start: 0.7309 (mtm-85) cc_final: 0.6864 (mtm-85) REVERT: C 179 MET cc_start: 0.8089 (tpt) cc_final: 0.7714 (tpp) REVERT: C 186 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8343 (m) REVERT: C 208 ARG cc_start: 0.7624 (ttp80) cc_final: 0.6392 (ttp-110) REVERT: B 36 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7708 (mp) REVERT: B 67 MET cc_start: 0.6953 (ptp) cc_final: 0.6687 (ptm) REVERT: B 71 ASP cc_start: 0.6389 (m-30) cc_final: 0.5924 (t70) REVERT: B 75 ASP cc_start: 0.7164 (m-30) cc_final: 0.6884 (m-30) REVERT: B 98 MET cc_start: 0.3799 (ptt) cc_final: 0.2197 (pmt) REVERT: B 135 ARG cc_start: 0.7577 (ttm-80) cc_final: 0.7318 (ttm170) REVERT: B 148 ASP cc_start: 0.8487 (m-30) cc_final: 0.8082 (m-30) REVERT: B 173 LYS cc_start: 0.7094 (pttp) cc_final: 0.6639 (mmpt) REVERT: F 25 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7917 (tp) REVERT: F 46 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7590 (mtpt) REVERT: G 30 MET cc_start: 0.8218 (ttp) cc_final: 0.7723 (tmm) REVERT: G 41 GLU cc_start: 0.7039 (tp30) cc_final: 0.6793 (mm-30) outliers start: 50 outliers final: 14 residues processed: 206 average time/residue: 1.3762 time to fit residues: 301.7883 Evaluate side-chains 211 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 36 LEU 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 48 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 103 THR Chi-restraints excluded: chain C residue 131 LEU 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 G residue 24 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 125 optimal weight: 0.0170 chunk 62 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2086 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= 0.211 Angle : 0.512 9.058 13549 Z= 0.265 Chirality : 0.037 0.122 1596 Planarity : 0.005 0.056 1729 Dihedral : 4.796 56.083 1384 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.13 % Allowed : 17.75 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1088 sheet: None (None), residues: 0 loop : 0.01 (0.44), residues: 210 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 0.029 0.002 PHE A 44 TYR 0.006 0.001 TYR D 237 ARG 0.007 0.000 ARG A 135 *********************** 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 225 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.2942 (OUTLIER) cc_final: 0.2267 (mt) REVERT: A 48 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6572 (mpp) REVERT: A 52 MET cc_start: 0.7142 (mmt) cc_final: 0.6867 (mmm) REVERT: A 195 MET cc_start: 0.8103 (mtp) cc_final: 0.7824 (mmm) REVERT: E 28 MET cc_start: 0.4888 (ptt) cc_final: 0.4547 (ptt) REVERT: E 52 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6734 (tpt) REVERT: E 59 THR cc_start: 0.7932 (m) cc_final: 0.7570 (p) REVERT: E 67 MET cc_start: 0.7023 (ptp) cc_final: 0.6518 (ptt) REVERT: E 83 MET cc_start: 0.5157 (mmm) cc_final: 0.4771 (mtp) REVERT: E 155 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8254 (tmm) REVERT: E 165 MET cc_start: 0.8418 (mtp) cc_final: 0.7971 (mtp) REVERT: E 173 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7172 (mmtt) REVERT: E 219 MET cc_start: 0.4688 (ttp) cc_final: 0.4041 (tpt) REVERT: D 49 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7205 (mttt) REVERT: D 60 LYS cc_start: 0.6132 (OUTLIER) cc_final: 0.5876 (mttp) REVERT: D 67 MET cc_start: 0.7966 (ptp) cc_final: 0.7712 (mtm) REVERT: D 83 MET cc_start: 0.5751 (mpp) cc_final: 0.5306 (mpp) REVERT: D 144 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7852 (ttm-80) REVERT: C 1 MET cc_start: 0.6227 (mmm) cc_final: 0.5940 (tpp) REVERT: C 64 LYS cc_start: 0.6526 (mmtm) cc_final: 0.6247 (mttm) REVERT: C 67 MET cc_start: 0.6825 (mtp) cc_final: 0.6025 (mmp) REVERT: C 131 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6355 (mm) REVERT: C 135 ARG cc_start: 0.7322 (mtm-85) cc_final: 0.7042 (mtm-85) REVERT: C 179 MET cc_start: 0.8058 (tpt) cc_final: 0.7739 (tpp) REVERT: C 186 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8340 (m) REVERT: C 208 ARG cc_start: 0.7629 (ttp80) cc_final: 0.6371 (ttp-110) REVERT: B 36 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7774 (mp) REVERT: B 52 MET cc_start: 0.7628 (mmm) cc_final: 0.7256 (mmt) REVERT: B 67 MET cc_start: 0.6998 (ptp) cc_final: 0.6734 (ptm) REVERT: B 71 ASP cc_start: 0.6410 (m-30) cc_final: 0.5951 (t70) REVERT: B 75 ASP cc_start: 0.7192 (m-30) cc_final: 0.6900 (m-30) REVERT: B 135 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.7243 (ttm170) REVERT: B 148 ASP cc_start: 0.8482 (m-30) cc_final: 0.8077 (m-30) REVERT: B 155 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7993 (tpt) REVERT: B 173 LYS cc_start: 0.7081 (pttp) cc_final: 0.6626 (mmpt) REVERT: F 25 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7908 (tp) REVERT: F 46 LYS cc_start: 0.7817 (mtmt) cc_final: 0.7560 (mtpp) REVERT: G 30 MET cc_start: 0.8221 (ttp) cc_final: 0.7709 (tmm) REVERT: G 41 GLU cc_start: 0.7083 (tp30) cc_final: 0.6805 (mm-30) outliers start: 43 outliers final: 14 residues processed: 198 average time/residue: 1.4011 time to fit residues: 295.1365 Evaluate side-chains 205 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 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 7 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 131 LEU 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 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 104 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10060 Z= 0.243 Angle : 0.522 7.531 13549 Z= 0.273 Chirality : 0.038 0.127 1596 Planarity : 0.005 0.057 1729 Dihedral : 4.717 59.459 1382 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.70 % Allowed : 17.56 % Favored : 77.74 % 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: 2.70 (0.23), residues: 1298 helix: 2.12 (0.15), residues: 1095 sheet: None (None), residues: 0 loop : -0.01 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 18 HIS 0.002 0.000 HIS C 136 PHE 0.017 0.002 PHE E 29 TYR 0.007 0.001 TYR C 241 ARG 0.008 0.000 ARG A 135 *********************** 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 234 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3007 (OUTLIER) cc_final: 0.2345 (mt) REVERT: A 32 VAL cc_start: 0.7572 (OUTLIER) cc_final: 0.7207 (t) REVERT: A 48 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6623 (mpp) REVERT: A 52 MET cc_start: 0.7184 (mmt) cc_final: 0.6939 (mmm) REVERT: A 64 LYS cc_start: 0.6360 (mttt) cc_final: 0.6007 (mtpt) REVERT: A 69 LYS cc_start: 0.6128 (tptp) cc_final: 0.5606 (mppt) REVERT: A 195 MET cc_start: 0.8120 (mtp) cc_final: 0.7784 (mmm) REVERT: E 28 MET cc_start: 0.4785 (ptt) cc_final: 0.4461 (ptt) REVERT: E 52 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6834 (tpt) REVERT: E 59 THR cc_start: 0.7924 (m) cc_final: 0.7487 (p) REVERT: E 67 MET cc_start: 0.7076 (ptp) cc_final: 0.6573 (ptt) REVERT: E 83 MET cc_start: 0.5085 (mmm) cc_final: 0.4831 (mtt) REVERT: E 155 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8259 (tmm) REVERT: E 165 MET cc_start: 0.8435 (mtp) cc_final: 0.8045 (mtp) REVERT: E 173 LYS cc_start: 0.7904 (mmtt) cc_final: 0.7178 (mmtt) REVERT: E 219 MET cc_start: 0.4702 (ttp) cc_final: 0.3981 (tpt) REVERT: D 49 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7237 (mttt) REVERT: D 60 LYS cc_start: 0.6217 (OUTLIER) cc_final: 0.5955 (mttp) REVERT: D 64 LYS cc_start: 0.7575 (ptpp) cc_final: 0.6171 (pptt) REVERT: D 67 MET cc_start: 0.7923 (ptp) cc_final: 0.7693 (mtm) REVERT: D 83 MET cc_start: 0.5798 (mpp) cc_final: 0.5371 (mpp) REVERT: D 144 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7856 (ttm-80) REVERT: D 173 LYS cc_start: 0.7638 (mttt) cc_final: 0.7337 (mttp) REVERT: C 64 LYS cc_start: 0.6555 (mmtm) cc_final: 0.6236 (mttm) REVERT: C 135 ARG cc_start: 0.7342 (mtm-85) cc_final: 0.7045 (mtm-85) REVERT: C 179 MET cc_start: 0.8055 (tpt) cc_final: 0.7729 (tpp) REVERT: C 186 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8351 (m) REVERT: C 208 ARG cc_start: 0.7626 (ttp80) cc_final: 0.6371 (ttp-110) REVERT: B 36 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7826 (mp) REVERT: B 67 MET cc_start: 0.7009 (ptp) cc_final: 0.6750 (ptm) REVERT: B 71 ASP cc_start: 0.6315 (m-30) cc_final: 0.5873 (t70) REVERT: B 75 ASP cc_start: 0.7165 (m-30) cc_final: 0.6874 (m-30) REVERT: B 135 ARG cc_start: 0.7586 (ttm-80) cc_final: 0.7296 (ttm170) REVERT: B 155 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8083 (tpt) REVERT: B 173 LYS cc_start: 0.7088 (pttp) cc_final: 0.6632 (mmpt) REVERT: F 25 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7910 (tp) REVERT: F 46 LYS cc_start: 0.7881 (mtmt) cc_final: 0.7589 (mtmt) REVERT: G 30 MET cc_start: 0.8238 (ttp) cc_final: 0.7734 (tmm) REVERT: G 41 GLU cc_start: 0.7024 (tp30) cc_final: 0.6737 (mm-30) outliers start: 49 outliers final: 17 residues processed: 211 average time/residue: 1.3917 time to fit residues: 312.6294 Evaluate side-chains 214 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 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 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 7 LEU 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 51 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 155 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 125 optimal weight: 0.0970 chunk 104 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2411 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= 0.210 Angle : 0.506 7.418 13549 Z= 0.264 Chirality : 0.037 0.122 1596 Planarity : 0.005 0.057 1729 Dihedral : 4.621 56.739 1382 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.61 % Allowed : 17.85 % 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: 2.85 (0.23), residues: 1298 helix: 2.24 (0.15), residues: 1095 sheet: None (None), residues: 0 loop : -0.01 (0.44), residues: 203 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 0.031 0.002 PHE A 44 TYR 0.006 0.001 TYR D 237 ARG 0.008 0.000 ARG A 135 *********************** 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 237 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3042 (OUTLIER) cc_final: 0.2355 (mt) REVERT: A 48 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6538 (mpp) REVERT: A 52 MET cc_start: 0.7179 (mmt) cc_final: 0.6932 (mmm) REVERT: A 64 LYS cc_start: 0.6389 (mttt) cc_final: 0.5963 (mtpt) REVERT: A 69 LYS cc_start: 0.6124 (tptp) cc_final: 0.5597 (mppt) REVERT: A 195 MET cc_start: 0.8099 (mtp) cc_final: 0.7763 (mmm) REVERT: E 28 MET cc_start: 0.4731 (ptt) cc_final: 0.4404 (ptt) REVERT: E 52 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6874 (tpt) REVERT: E 59 THR cc_start: 0.7872 (m) cc_final: 0.7396 (p) REVERT: E 67 MET cc_start: 0.7093 (ptp) cc_final: 0.6611 (ptt) REVERT: E 155 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8253 (tmm) REVERT: E 165 MET cc_start: 0.8431 (mtp) cc_final: 0.8093 (mtp) REVERT: E 173 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7175 (mmtt) REVERT: E 219 MET cc_start: 0.4657 (ttp) cc_final: 0.4006 (tpt) REVERT: D 49 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7208 (mttt) REVERT: D 60 LYS cc_start: 0.6234 (OUTLIER) cc_final: 0.5950 (mttp) REVERT: D 64 LYS cc_start: 0.7549 (ptpp) cc_final: 0.6115 (pptt) REVERT: D 83 MET cc_start: 0.5781 (OUTLIER) cc_final: 0.5353 (mpp) REVERT: D 144 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7867 (ttm-80) REVERT: D 173 LYS cc_start: 0.7591 (mttt) cc_final: 0.7294 (mttp) REVERT: C 1 MET cc_start: 0.6106 (mmm) cc_final: 0.5862 (tpp) REVERT: C 64 LYS cc_start: 0.6501 (mmtm) cc_final: 0.6197 (mttm) REVERT: C 67 MET cc_start: 0.6997 (mtp) cc_final: 0.6081 (mmp) REVERT: C 135 ARG cc_start: 0.7281 (mtm-85) cc_final: 0.7012 (mtm-85) REVERT: C 179 MET cc_start: 0.8044 (tpt) cc_final: 0.7653 (tpp) REVERT: C 186 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8346 (m) REVERT: C 208 ARG cc_start: 0.7645 (ttp80) cc_final: 0.6465 (ttp-110) REVERT: B 36 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7776 (mp) REVERT: B 52 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7190 (mmt) REVERT: B 67 MET cc_start: 0.7037 (ptp) cc_final: 0.6788 (ptm) REVERT: B 71 ASP cc_start: 0.6316 (m-30) cc_final: 0.5876 (t70) REVERT: B 75 ASP cc_start: 0.7182 (m-30) cc_final: 0.6882 (m-30) REVERT: B 135 ARG cc_start: 0.7570 (ttm-80) cc_final: 0.7362 (ttm170) REVERT: B 155 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8008 (tpt) REVERT: B 173 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6616 (mmpt) REVERT: F 25 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7903 (tp) REVERT: F 46 LYS cc_start: 0.7922 (mtmt) cc_final: 0.7688 (mtpt) REVERT: G 30 MET cc_start: 0.8224 (ttp) cc_final: 0.7666 (tmm) REVERT: G 41 GLU cc_start: 0.6999 (tp30) cc_final: 0.6735 (mm-30) outliers start: 48 outliers final: 16 residues processed: 210 average time/residue: 1.3838 time to fit residues: 309.5848 Evaluate side-chains 214 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 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 83 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.5980 chunk 14 optimal weight: 0.0770 chunk 71 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2528 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= 0.195 Angle : 0.503 7.157 13549 Z= 0.262 Chirality : 0.037 0.133 1596 Planarity : 0.005 0.057 1729 Dihedral : 4.583 56.199 1382 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.84 % Allowed : 18.71 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.97 (0.23), residues: 1298 helix: 2.31 (0.15), residues: 1101 sheet: None (None), residues: 0 loop : -0.02 (0.44), residues: 197 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 0.015 0.001 PHE F 39 TYR 0.005 0.001 TYR D 237 ARG 0.008 0.000 ARG A 135 *********************** 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 226 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.2912 (OUTLIER) cc_final: 0.2314 (mt) REVERT: A 32 VAL cc_start: 0.7539 (OUTLIER) cc_final: 0.7178 (t) REVERT: A 48 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6560 (mpp) REVERT: A 52 MET cc_start: 0.7123 (mmt) cc_final: 0.6848 (mmm) REVERT: A 64 LYS cc_start: 0.6469 (mttt) cc_final: 0.6010 (mtmt) REVERT: A 69 LYS cc_start: 0.6120 (tptp) cc_final: 0.5587 (mppt) REVERT: A 195 MET cc_start: 0.8103 (mtp) cc_final: 0.7772 (mmm) REVERT: E 28 MET cc_start: 0.4621 (ptt) cc_final: 0.4323 (ptt) REVERT: E 52 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6933 (tpt) REVERT: E 59 THR cc_start: 0.7865 (m) cc_final: 0.7378 (p) REVERT: E 67 MET cc_start: 0.7130 (ptp) cc_final: 0.6652 (ptt) REVERT: E 155 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8244 (tmm) REVERT: E 165 MET cc_start: 0.8412 (mtp) cc_final: 0.8006 (mtp) REVERT: E 173 LYS cc_start: 0.7980 (mmtt) cc_final: 0.7197 (mmtt) REVERT: E 219 MET cc_start: 0.4732 (ttp) cc_final: 0.4020 (tpt) REVERT: D 49 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7202 (mttt) REVERT: D 64 LYS cc_start: 0.7491 (ptpp) cc_final: 0.6156 (pptt) REVERT: D 144 ARG cc_start: 0.8120 (ttm-80) cc_final: 0.7864 (ttm-80) REVERT: D 173 LYS cc_start: 0.7612 (mttt) cc_final: 0.7314 (mttp) REVERT: C 1 MET cc_start: 0.6173 (mmm) cc_final: 0.5891 (tpp) REVERT: C 64 LYS cc_start: 0.6515 (mmtm) cc_final: 0.6193 (mttm) REVERT: C 67 MET cc_start: 0.7041 (mtp) cc_final: 0.6103 (mmp) REVERT: C 135 ARG cc_start: 0.7265 (mtm-85) cc_final: 0.7008 (mtm-85) REVERT: C 179 MET cc_start: 0.8032 (tpt) cc_final: 0.7633 (tpp) REVERT: C 186 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8337 (m) REVERT: C 208 ARG cc_start: 0.7678 (ttp80) cc_final: 0.6496 (ttp-110) REVERT: B 36 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7784 (mp) REVERT: B 52 MET cc_start: 0.7554 (mmm) cc_final: 0.7191 (mmt) REVERT: B 67 MET cc_start: 0.7047 (ptp) cc_final: 0.6799 (ptm) REVERT: B 71 ASP cc_start: 0.6316 (m-30) cc_final: 0.5874 (t70) REVERT: B 75 ASP cc_start: 0.7189 (m-30) cc_final: 0.6885 (m-30) REVERT: B 155 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8012 (tpt) REVERT: B 173 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6653 (mmpt) REVERT: F 25 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7901 (tp) REVERT: F 41 GLU cc_start: 0.6286 (mm-30) cc_final: 0.5895 (pt0) REVERT: G 30 MET cc_start: 0.8222 (ttp) cc_final: 0.7661 (tmm) REVERT: G 41 GLU cc_start: 0.6921 (tp30) cc_final: 0.6614 (mm-30) outliers start: 40 outliers final: 15 residues processed: 204 average time/residue: 1.4216 time to fit residues: 307.9679 Evaluate side-chains 209 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 155 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 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 50 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 120 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10060 Z= 0.213 Angle : 0.520 8.685 13549 Z= 0.270 Chirality : 0.037 0.122 1596 Planarity : 0.005 0.057 1729 Dihedral : 4.604 55.086 1382 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.55 % Allowed : 19.29 % Favored : 77.16 % 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: 2.97 (0.23), residues: 1298 helix: 2.31 (0.15), residues: 1101 sheet: None (None), residues: 0 loop : -0.02 (0.44), residues: 197 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 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.2939 (OUTLIER) cc_final: 0.2343 (mt) REVERT: A 32 VAL cc_start: 0.7540 (OUTLIER) cc_final: 0.7177 (t) REVERT: A 48 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6535 (mpp) REVERT: A 52 MET cc_start: 0.7167 (mmt) cc_final: 0.6867 (mmm) REVERT: A 64 LYS cc_start: 0.6468 (mttt) cc_final: 0.5981 (mtmt) REVERT: A 69 LYS cc_start: 0.6157 (tptp) cc_final: 0.5633 (mppt) REVERT: A 195 MET cc_start: 0.8105 (mtp) cc_final: 0.7769 (mmm) REVERT: E 28 MET cc_start: 0.4648 (ptt) cc_final: 0.4356 (ptt) REVERT: E 52 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.7031 (tpt) REVERT: E 67 MET cc_start: 0.7153 (ptp) cc_final: 0.6677 (ptt) REVERT: E 155 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8254 (tmm) REVERT: E 165 MET cc_start: 0.8425 (mtp) cc_final: 0.7965 (mtp) REVERT: E 173 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7197 (mmtt) REVERT: E 219 MET cc_start: 0.4697 (ttp) cc_final: 0.3963 (tpt) REVERT: D 49 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7194 (mttt) REVERT: D 64 LYS cc_start: 0.7479 (ptpp) cc_final: 0.6202 (pptt) REVERT: D 83 MET cc_start: 0.5506 (mmm) cc_final: 0.5276 (mmm) REVERT: D 173 LYS cc_start: 0.7602 (mttt) cc_final: 0.7306 (mttp) REVERT: C 1 MET cc_start: 0.6204 (mmm) cc_final: 0.5912 (tpp) REVERT: C 64 LYS cc_start: 0.6534 (mmtm) cc_final: 0.6203 (mttm) REVERT: C 135 ARG cc_start: 0.7265 (mtm-85) cc_final: 0.6987 (mtm-85) REVERT: C 144 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8100 (mmt90) REVERT: C 179 MET cc_start: 0.8048 (tpt) cc_final: 0.7653 (tpp) REVERT: C 186 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8345 (m) REVERT: C 208 ARG cc_start: 0.7634 (ttp80) cc_final: 0.6455 (ttp-110) REVERT: B 36 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7810 (mp) REVERT: B 52 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7190 (mmt) REVERT: B 67 MET cc_start: 0.7073 (ptp) cc_final: 0.6820 (ptm) REVERT: B 71 ASP cc_start: 0.6324 (m-30) cc_final: 0.5876 (t70) REVERT: B 75 ASP cc_start: 0.7196 (m-30) cc_final: 0.6895 (m-30) REVERT: B 155 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7990 (tpt) REVERT: B 173 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6692 (mmpt) REVERT: F 25 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7905 (tp) REVERT: F 41 GLU cc_start: 0.6268 (mm-30) cc_final: 0.5914 (pt0) REVERT: G 30 MET cc_start: 0.8251 (ttp) cc_final: 0.7672 (tmm) REVERT: G 41 GLU cc_start: 0.6882 (tp30) cc_final: 0.6572 (mm-30) outliers start: 37 outliers final: 17 residues processed: 201 average time/residue: 1.4277 time to fit residues: 304.8338 Evaluate side-chains 214 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 144 ARG 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 52 MET Chi-restraints excluded: chain B residue 155 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 F residue 55 LYS Chi-restraints excluded: chain G residue 24 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 120 optimal weight: 0.0000 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 123 optimal weight: 0.4980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10060 Z= 0.181 Angle : 0.496 6.774 13549 Z= 0.258 Chirality : 0.036 0.122 1596 Planarity : 0.005 0.056 1729 Dihedral : 4.534 55.760 1382 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.07 % Allowed : 19.77 % Favored : 77.16 % 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: 3.14 (0.23), residues: 1298 helix: 2.41 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : 0.12 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 18 HIS 0.001 0.000 HIS C 136 PHE 0.015 0.001 PHE F 39 TYR 0.005 0.001 TYR E 241 ARG 0.008 0.000 ARG A 135 *********************** 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 217 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.2837 (OUTLIER) cc_final: 0.2249 (mt) REVERT: A 32 VAL cc_start: 0.7537 (OUTLIER) cc_final: 0.7177 (t) REVERT: A 48 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6616 (mpp) REVERT: A 52 MET cc_start: 0.7170 (mmt) cc_final: 0.6881 (mmm) REVERT: A 64 LYS cc_start: 0.6515 (mttt) cc_final: 0.6053 (mtpt) REVERT: A 69 LYS cc_start: 0.6177 (tptp) cc_final: 0.5664 (mppt) REVERT: A 153 MET cc_start: 0.8382 (mmm) cc_final: 0.8160 (mmm) REVERT: A 195 MET cc_start: 0.8094 (mtp) cc_final: 0.7765 (mmm) REVERT: E 28 MET cc_start: 0.4417 (ptt) cc_final: 0.4146 (ptt) REVERT: E 67 MET cc_start: 0.7137 (ptp) cc_final: 0.6665 (ptt) REVERT: E 83 MET cc_start: 0.4909 (ttm) cc_final: 0.4006 (tpp) REVERT: E 155 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8241 (tmm) REVERT: E 165 MET cc_start: 0.8408 (mtp) cc_final: 0.8011 (mtp) REVERT: E 173 LYS cc_start: 0.7979 (mmtt) cc_final: 0.7186 (mmtt) REVERT: E 219 MET cc_start: 0.4703 (ttp) cc_final: 0.3970 (tpt) REVERT: D 49 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7160 (mttt) REVERT: D 64 LYS cc_start: 0.7523 (ptpp) cc_final: 0.6188 (pptt) REVERT: D 83 MET cc_start: 0.5405 (mmm) cc_final: 0.5171 (mmm) REVERT: D 173 LYS cc_start: 0.7528 (mttt) cc_final: 0.7240 (mttp) REVERT: C 1 MET cc_start: 0.6252 (mmm) cc_final: 0.5950 (tpp) REVERT: C 64 LYS cc_start: 0.6532 (mmtm) cc_final: 0.6192 (mttm) REVERT: C 135 ARG cc_start: 0.7249 (mtm-85) cc_final: 0.6979 (mtm-85) REVERT: C 179 MET cc_start: 0.8025 (tpt) cc_final: 0.7609 (tpp) REVERT: C 186 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8337 (m) REVERT: C 208 ARG cc_start: 0.7669 (ttp80) cc_final: 0.6487 (ttp-110) REVERT: B 36 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7821 (mp) REVERT: B 52 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7192 (mmt) REVERT: B 67 MET cc_start: 0.7095 (ptp) cc_final: 0.6855 (ptm) REVERT: B 71 ASP cc_start: 0.6338 (m-30) cc_final: 0.5896 (t70) REVERT: B 75 ASP cc_start: 0.7197 (m-30) cc_final: 0.6893 (m-30) REVERT: B 173 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6684 (mmpt) REVERT: F 25 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7899 (tp) REVERT: F 55 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6646 (ttmt) REVERT: G 30 MET cc_start: 0.8251 (ttp) cc_final: 0.7659 (tmm) REVERT: G 41 GLU cc_start: 0.6862 (tp30) cc_final: 0.5346 (pm20) outliers start: 32 outliers final: 11 residues processed: 197 average time/residue: 1.4391 time to fit residues: 301.4982 Evaluate side-chains 204 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 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 F residue 55 LYS Chi-restraints excluded: chain G residue 24 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10060 Z= 0.245 Angle : 0.550 9.683 13549 Z= 0.282 Chirality : 0.038 0.144 1596 Planarity : 0.005 0.057 1729 Dihedral : 4.634 53.969 1382 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.88 % Allowed : 20.44 % Favored : 76.68 % 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: 2.86 (0.23), residues: 1298 helix: 2.20 (0.15), residues: 1110 sheet: None (None), residues: 0 loop : 0.08 (0.45), residues: 188 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 0.030 0.002 PHE A 44 TYR 0.006 0.001 TYR D 237 ARG 0.008 0.000 ARG A 135 ********************** 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 212 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.2947 (OUTLIER) cc_final: 0.2352 (mt) REVERT: A 32 VAL cc_start: 0.7543 (OUTLIER) cc_final: 0.7175 (t) REVERT: A 48 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6537 (mpp) REVERT: A 52 MET cc_start: 0.7207 (mmt) cc_final: 0.6931 (mmm) REVERT: A 195 MET cc_start: 0.8129 (mtp) cc_final: 0.7782 (mmm) REVERT: E 28 MET cc_start: 0.4568 (ptt) cc_final: 0.4294 (ptt) REVERT: E 67 MET cc_start: 0.7154 (ptp) cc_final: 0.6675 (ptt) REVERT: E 83 MET cc_start: 0.4725 (ttm) cc_final: 0.4236 (tpt) REVERT: E 155 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8259 (tmm) REVERT: E 165 MET cc_start: 0.8443 (mtp) cc_final: 0.8051 (mtp) REVERT: E 173 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7229 (mmtt) REVERT: E 219 MET cc_start: 0.4685 (ttp) cc_final: 0.4012 (tpt) REVERT: D 49 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7227 (mttt) REVERT: D 64 LYS cc_start: 0.7492 (ptpp) cc_final: 0.6162 (pptt) REVERT: D 83 MET cc_start: 0.5451 (mmm) cc_final: 0.5174 (mmm) REVERT: D 173 LYS cc_start: 0.7634 (mttt) cc_final: 0.7323 (mttp) REVERT: C 64 LYS cc_start: 0.6553 (mmtm) cc_final: 0.6211 (mttm) REVERT: C 135 ARG cc_start: 0.7258 (mtm-85) cc_final: 0.6984 (mtm-85) REVERT: C 144 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8133 (mmt90) REVERT: C 179 MET cc_start: 0.8073 (tpt) cc_final: 0.7686 (tpp) REVERT: C 186 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8362 (m) REVERT: C 208 ARG cc_start: 0.7607 (ttp80) cc_final: 0.6460 (ttp-110) REVERT: B 36 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7850 (mp) REVERT: B 52 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7190 (mmt) REVERT: B 67 MET cc_start: 0.7107 (ptp) cc_final: 0.6857 (ptm) REVERT: B 71 ASP cc_start: 0.6318 (m-30) cc_final: 0.5891 (t70) REVERT: B 75 ASP cc_start: 0.7209 (m-30) cc_final: 0.6907 (m-30) REVERT: B 173 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6702 (mmpt) REVERT: F 25 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7903 (tp) REVERT: F 41 GLU cc_start: 0.6381 (mm-30) cc_final: 0.5991 (pt0) REVERT: G 30 MET cc_start: 0.8262 (ttp) cc_final: 0.7672 (tmm) REVERT: G 41 GLU cc_start: 0.6874 (tp30) cc_final: 0.6572 (mm-30) outliers start: 30 outliers final: 12 residues processed: 199 average time/residue: 1.4186 time to fit residues: 299.9725 Evaluate side-chains 199 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 144 ARG 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 90 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 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 C 138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.235557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.155957 restraints weight = 8483.710| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.50 r_work: 0.3584 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2776 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= 0.209 Angle : 0.537 9.083 13549 Z= 0.274 Chirality : 0.037 0.171 1596 Planarity : 0.005 0.057 1729 Dihedral : 4.590 54.025 1382 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.59 % Allowed : 21.02 % Favored : 76.39 % 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: 2.87 (0.23), residues: 1298 helix: 2.21 (0.15), residues: 1117 sheet: None (None), residues: 0 loop : 0.02 (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 C 136 PHE 0.015 0.001 PHE F 39 TYR 0.005 0.001 TYR D 237 ARG 0.008 0.000 ARG A 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5009.80 seconds wall clock time: 89 minutes 53.71 seconds (5393.71 seconds total)