Starting phenix.real_space_refine on Wed Feb 14 17:56:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brd_16212/02_2024/8brd_16212.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brd_16212/02_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_16212/02_2024/8brd_16212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brd_16212/02_2024/8brd_16212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brd_16212/02_2024/8brd_16212.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8brd_16212/02_2024/8brd_16212.pdb" } 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 Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "E TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B GLU 250": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.57, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 4.32 Conformation dependent library (CDL) restraints added in 1.9 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: 0.91 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: 3.13 Time building geometry restraints manager: 4.64 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: 89.04 - 98.60: 5 98.60 - 108.16: 302 108.16 - 117.72: 7228 117.72 - 127.28: 5970 127.28 - 136.84: 44 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 2.440 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 20 through 243) selection = (chain 'B' and resid 20 through 243) selection = (chain 'C' and resid 20 through 243) selection = (chain 'D' and resid 20 through 243) selection = (chain 'E' and resid 20 through 243) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 11 through 61) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 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: 14.010 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 30.340 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.070 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 30 poor density : 214 time to evaluate : 1.084 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: 1.3801 time to fit residues: 336.5995 Evaluate side-chains 206 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 189 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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: 0.5980 chunk 98 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 118 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 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10060 Z= 0.214 Angle : 0.535 6.756 13549 Z= 0.278 Chirality : 0.038 0.132 1596 Planarity : 0.005 0.066 1729 Dihedral : 5.366 52.907 1402 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.18 % Allowed : 17.56 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.23), residues: 1298 helix: 2.03 (0.16), residues: 1103 sheet: None (None), residues: 0 loop : -0.20 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 18 HIS 0.002 0.001 HIS A 136 PHE 0.024 0.002 PHE A 44 TYR 0.006 0.001 TYR D 237 ARG 0.006 0.000 ARG A 135 *********************** 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 fitting. rotamer outliers: 54 poor density : 188 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LEU cc_start: 0.2687 (OUTLIER) cc_final: 0.2374 (pp) REVERT: A 9 LEU cc_start: 0.3136 (OUTLIER) cc_final: 0.2404 (mt) REVERT: A 48 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6708 (mpp) REVERT: A 52 MET cc_start: 0.7117 (mmt) cc_final: 0.6854 (mmm) REVERT: A 195 MET cc_start: 0.8014 (mtp) cc_final: 0.7761 (mmm) REVERT: E 36 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7748 (mt) REVERT: E 67 MET cc_start: 0.6831 (ptp) cc_final: 0.6286 (ptt) REVERT: E 155 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8287 (tmm) REVERT: E 165 MET cc_start: 0.8385 (mtp) cc_final: 0.7940 (mtp) REVERT: E 173 LYS cc_start: 0.7825 (mmtt) cc_final: 0.7228 (mmtt) REVERT: E 219 MET cc_start: 0.4660 (ttp) cc_final: 0.4039 (tpt) REVERT: D 48 MET cc_start: 0.7283 (mtp) cc_final: 0.6988 (mmm) REVERT: D 49 LYS cc_start: 0.7620 (mtpt) cc_final: 0.7245 (mttt) REVERT: D 67 MET cc_start: 0.7922 (ptp) cc_final: 0.7657 (mtm) REVERT: D 144 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7805 (ttm-80) REVERT: D 153 MET cc_start: 0.8357 (mmm) cc_final: 0.8079 (tpp) REVERT: C 1 MET cc_start: 0.6139 (mmm) cc_final: 0.5817 (tpp) REVERT: C 64 LYS cc_start: 0.6576 (mmtm) cc_final: 0.6352 (mttm) REVERT: C 67 MET cc_start: 0.6765 (mtp) cc_final: 0.5897 (mmp) REVERT: C 126 LYS cc_start: 0.7154 (mmmt) cc_final: 0.6576 (mttp) REVERT: C 131 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6461 (mm) REVERT: C 135 ARG cc_start: 0.7303 (mtm-85) cc_final: 0.6874 (mtm-85) REVERT: C 179 MET cc_start: 0.8063 (tpt) cc_final: 0.7796 (tpp) REVERT: C 186 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8380 (m) REVERT: C 203 LYS cc_start: 0.8090 (tppt) cc_final: 0.7859 (tptt) REVERT: C 208 ARG cc_start: 0.7548 (ttp80) cc_final: 0.6544 (ttp-110) REVERT: C 211 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6752 (mm-30) REVERT: B 36 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7615 (mp) REVERT: B 52 MET cc_start: 0.7587 (mmm) cc_final: 0.7210 (mmt) REVERT: B 67 MET cc_start: 0.6922 (ptp) cc_final: 0.6658 (ptm) REVERT: B 71 ASP cc_start: 0.6193 (m-30) cc_final: 0.5788 (t70) REVERT: B 75 ASP cc_start: 0.7182 (m-30) cc_final: 0.6964 (m-30) REVERT: B 173 LYS cc_start: 0.7010 (pttp) cc_final: 0.6670 (mmpt) REVERT: B 202 ASP cc_start: 0.7596 (m-30) cc_final: 0.7368 (m-30) REVERT: F 25 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7968 (tp) REVERT: F 46 LYS cc_start: 0.7778 (mtmt) cc_final: 0.7478 (mtmt) REVERT: G 30 MET cc_start: 0.8207 (ttp) cc_final: 0.7775 (tmm) REVERT: G 41 GLU cc_start: 0.6941 (tp30) cc_final: 0.6582 (tm-30) outliers start: 54 outliers final: 13 residues processed: 212 average time/residue: 1.3350 time to fit residues: 302.7783 Evaluate side-chains 204 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 118 optimal weight: 0.0980 chunk 127 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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: 0.7632 moved from start: 0.1752 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= 0.194 Angle : 0.500 7.684 13549 Z= 0.259 Chirality : 0.037 0.125 1596 Planarity : 0.004 0.053 1729 Dihedral : 4.721 47.718 1384 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.32 % Allowed : 18.91 % Favored : 76.78 % 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: 2.16 (0.15), residues: 1097 sheet: None (None), residues: 0 loop : 0.07 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 18 HIS 0.001 0.000 HIS B 116 PHE 0.017 0.001 PHE F 39 TYR 0.006 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 229 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 184 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3160 (OUTLIER) cc_final: 0.2489 (mt) REVERT: A 48 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6682 (mpp) REVERT: A 52 MET cc_start: 0.7147 (mmt) cc_final: 0.6866 (mmm) REVERT: A 195 MET cc_start: 0.8045 (mtp) cc_final: 0.7760 (mmm) REVERT: E 36 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7694 (mt) REVERT: E 52 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6721 (tpt) REVERT: E 67 MET cc_start: 0.6919 (ptp) cc_final: 0.6422 (ptt) REVERT: E 155 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8294 (tmm) REVERT: E 165 MET cc_start: 0.8369 (mtp) cc_final: 0.7968 (mtp) REVERT: E 173 LYS cc_start: 0.7830 (mmtt) cc_final: 0.7171 (mmtt) REVERT: E 219 MET cc_start: 0.4676 (ttp) cc_final: 0.4059 (tpt) REVERT: D 49 LYS cc_start: 0.7597 (mtpt) cc_final: 0.7192 (mttt) REVERT: D 67 MET cc_start: 0.7946 (ptp) cc_final: 0.7706 (mtm) REVERT: D 83 MET cc_start: 0.5794 (mpp) cc_final: 0.5393 (mpp) REVERT: D 144 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.7806 (ttm-80) REVERT: D 153 MET cc_start: 0.8323 (mmm) cc_final: 0.8073 (tpp) REVERT: C 1 MET cc_start: 0.6180 (mmm) cc_final: 0.5894 (tpp) REVERT: C 64 LYS cc_start: 0.6512 (mmtm) cc_final: 0.6256 (mttm) REVERT: C 67 MET cc_start: 0.6814 (mtp) cc_final: 0.6044 (mmp) REVERT: C 126 LYS cc_start: 0.7144 (mmmt) cc_final: 0.6575 (mttp) REVERT: C 131 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6467 (mm) REVERT: C 135 ARG cc_start: 0.7350 (mtm-85) cc_final: 0.6904 (mtm-85) REVERT: C 179 MET cc_start: 0.8053 (tpt) cc_final: 0.7683 (tpp) REVERT: C 186 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8403 (m) REVERT: C 208 ARG cc_start: 0.7584 (ttp80) cc_final: 0.6522 (ttp-110) REVERT: B 36 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7766 (mp) REVERT: B 52 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7184 (mmt) REVERT: B 67 MET cc_start: 0.6964 (ptp) cc_final: 0.6716 (ptm) REVERT: B 71 ASP cc_start: 0.6212 (m-30) cc_final: 0.5801 (t70) REVERT: B 75 ASP cc_start: 0.7256 (m-30) cc_final: 0.7040 (m-30) REVERT: B 98 MET cc_start: 0.3686 (ptt) cc_final: 0.2096 (pmt) REVERT: B 148 ASP cc_start: 0.8479 (m-30) cc_final: 0.8051 (m-30) REVERT: B 155 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7978 (tpt) REVERT: B 173 LYS cc_start: 0.7027 (pttp) cc_final: 0.6610 (mmpt) REVERT: B 202 ASP cc_start: 0.7557 (m-30) cc_final: 0.7334 (m-30) REVERT: F 25 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7909 (tp) REVERT: F 41 GLU cc_start: 0.6451 (mm-30) cc_final: 0.5959 (pt0) REVERT: F 46 LYS cc_start: 0.7830 (mtmt) cc_final: 0.7608 (mtpt) REVERT: G 30 MET cc_start: 0.8204 (ttp) cc_final: 0.7713 (tmm) REVERT: G 41 GLU cc_start: 0.6955 (tp30) cc_final: 0.6685 (mm-30) outliers start: 45 outliers final: 11 residues processed: 204 average time/residue: 1.3047 time to fit residues: 283.8767 Evaluate side-chains 200 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET 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 52 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 33 optimal weight: 0.0470 overall best weight: 0.9280 ------------------------------------------------------------------------------- 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 F 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10060 Z= 0.257 Angle : 0.543 8.532 13549 Z= 0.281 Chirality : 0.038 0.136 1596 Planarity : 0.005 0.055 1729 Dihedral : 4.896 57.509 1384 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.99 % Allowed : 17.85 % 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: 2.63 (0.23), residues: 1298 helix: 2.05 (0.15), residues: 1096 sheet: None (None), residues: 0 loop : 0.12 (0.44), residues: 202 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 0.028 0.002 PHE A 44 TYR 0.008 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 234 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 182 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3010 (OUTLIER) cc_final: 0.2345 (mt) REVERT: A 32 VAL cc_start: 0.7505 (OUTLIER) cc_final: 0.7139 (t) REVERT: A 48 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6590 (mpp) REVERT: A 52 MET cc_start: 0.7186 (mmt) cc_final: 0.6926 (mmm) REVERT: A 64 LYS cc_start: 0.6290 (mttt) cc_final: 0.5974 (mtpt) REVERT: A 69 LYS cc_start: 0.6239 (tptp) cc_final: 0.5797 (mppt) REVERT: A 195 MET cc_start: 0.8125 (mtp) cc_final: 0.7803 (mmm) REVERT: A 208 ARG cc_start: 0.6905 (ttp-110) cc_final: 0.6673 (ttp80) REVERT: E 28 MET cc_start: 0.4982 (ptt) cc_final: 0.4610 (ptt) REVERT: E 52 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6795 (tpt) REVERT: E 67 MET cc_start: 0.7054 (ptp) cc_final: 0.6540 (ptt) REVERT: E 155 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8254 (tmm) REVERT: E 165 MET cc_start: 0.8449 (mtp) cc_final: 0.8064 (mtp) REVERT: E 173 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7177 (mmtt) REVERT: E 219 MET cc_start: 0.4713 (ttp) cc_final: 0.4058 (tpt) REVERT: D 49 LYS cc_start: 0.7651 (mtpt) cc_final: 0.7216 (mttt) REVERT: D 60 LYS cc_start: 0.6304 (OUTLIER) cc_final: 0.5944 (mttp) REVERT: D 67 MET cc_start: 0.7932 (ptp) cc_final: 0.7649 (mtm) REVERT: D 83 MET cc_start: 0.5802 (mpp) cc_final: 0.5326 (mpp) REVERT: D 144 ARG cc_start: 0.8187 (ttm-80) cc_final: 0.7831 (ttm-80) REVERT: D 153 MET cc_start: 0.8330 (mmm) cc_final: 0.8070 (tpp) REVERT: C 64 LYS cc_start: 0.6532 (mmtm) cc_final: 0.6233 (mttm) REVERT: C 67 MET cc_start: 0.6834 (mtp) cc_final: 0.6077 (mmp) REVERT: C 135 ARG cc_start: 0.7359 (mtm-85) cc_final: 0.7055 (mtm-85) REVERT: C 179 MET cc_start: 0.8072 (tpt) cc_final: 0.7733 (tpp) REVERT: C 186 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8390 (m) REVERT: C 208 ARG cc_start: 0.7598 (ttp80) cc_final: 0.6370 (ttp-110) REVERT: B 36 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7749 (mp) REVERT: B 67 MET cc_start: 0.6995 (ptp) cc_final: 0.6726 (ptm) REVERT: B 71 ASP cc_start: 0.6204 (m-30) cc_final: 0.5790 (t70) REVERT: B 75 ASP cc_start: 0.7277 (m-30) cc_final: 0.7075 (m-30) REVERT: B 155 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8123 (tpt) REVERT: B 173 LYS cc_start: 0.7011 (pttp) cc_final: 0.6806 (mtmm) REVERT: F 25 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7908 (tp) REVERT: F 41 GLU cc_start: 0.6437 (mm-30) cc_final: 0.5962 (pt0) REVERT: F 46 LYS cc_start: 0.7869 (mtmt) cc_final: 0.7587 (mtmt) REVERT: G 30 MET cc_start: 0.8239 (ttp) cc_final: 0.7732 (tmm) REVERT: G 41 GLU cc_start: 0.7039 (tp30) cc_final: 0.6716 (mm-30) outliers start: 52 outliers final: 18 residues processed: 208 average time/residue: 1.4074 time to fit residues: 311.1449 Evaluate side-chains 209 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 181 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 61 ILE Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 144 ARG Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain D residue 20 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 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: 4.9990 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 112 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 B 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 10060 Z= 0.286 Angle : 0.553 8.407 13549 Z= 0.287 Chirality : 0.039 0.134 1596 Planarity : 0.005 0.059 1729 Dihedral : 4.757 51.708 1382 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.18 % Allowed : 18.14 % 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: 2.56 (0.23), residues: 1298 helix: 2.00 (0.15), residues: 1101 sheet: None (None), residues: 0 loop : 0.09 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP F 18 HIS 0.002 0.001 HIS C 136 PHE 0.018 0.002 PHE A 143 TYR 0.008 0.001 TYR D 237 ARG 0.007 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 242 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 188 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3023 (OUTLIER) cc_final: 0.2332 (mt) REVERT: A 32 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7147 (t) REVERT: A 48 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6560 (mpp) REVERT: A 52 MET cc_start: 0.7271 (mmt) cc_final: 0.6986 (mmm) REVERT: A 64 LYS cc_start: 0.6468 (mttt) cc_final: 0.6008 (mtpt) REVERT: A 69 LYS cc_start: 0.6294 (tptp) cc_final: 0.5809 (mppt) REVERT: A 195 MET cc_start: 0.8115 (mtp) cc_final: 0.7790 (mmm) REVERT: E 28 MET cc_start: 0.4931 (ptt) cc_final: 0.4573 (ptt) REVERT: E 52 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6875 (tpt) REVERT: E 67 MET cc_start: 0.7116 (ptp) cc_final: 0.6612 (ptt) REVERT: E 155 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8261 (tmm) REVERT: E 165 MET cc_start: 0.8452 (mtp) cc_final: 0.8091 (mtp) REVERT: E 173 LYS cc_start: 0.7950 (mmtt) cc_final: 0.7193 (mmtt) REVERT: E 179 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8252 (tpt) REVERT: E 219 MET cc_start: 0.4668 (ttp) cc_final: 0.4015 (tpt) REVERT: D 49 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7200 (mttt) REVERT: D 64 LYS cc_start: 0.7628 (ptpp) cc_final: 0.6140 (pptt) REVERT: D 83 MET cc_start: 0.5740 (mpp) cc_final: 0.5344 (mpp) REVERT: D 144 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7906 (ttm-80) REVERT: D 153 MET cc_start: 0.8360 (mmm) cc_final: 0.8097 (tpp) REVERT: C 28 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8330 (ptm) REVERT: C 64 LYS cc_start: 0.6522 (mmtm) cc_final: 0.6196 (mttm) REVERT: C 67 MET cc_start: 0.6903 (mtp) cc_final: 0.6159 (mmp) REVERT: C 135 ARG cc_start: 0.7301 (mtm-85) cc_final: 0.7020 (mtm-85) REVERT: C 179 MET cc_start: 0.8090 (tpt) cc_final: 0.7736 (tpp) REVERT: C 186 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8422 (m) REVERT: C 208 ARG cc_start: 0.7591 (ttp80) cc_final: 0.6468 (ttp-110) REVERT: B 36 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7725 (mp) REVERT: B 67 MET cc_start: 0.7052 (ptp) cc_final: 0.6777 (ptm) REVERT: B 71 ASP cc_start: 0.6235 (m-30) cc_final: 0.5810 (t70) REVERT: B 117 ASP cc_start: 0.5938 (OUTLIER) cc_final: 0.5253 (t70) REVERT: B 155 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8058 (tpt) REVERT: B 173 LYS cc_start: 0.7079 (pttp) cc_final: 0.6858 (mtmm) REVERT: F 25 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7920 (tp) REVERT: F 41 GLU cc_start: 0.6444 (mm-30) cc_final: 0.5937 (pt0) REVERT: G 30 MET cc_start: 0.8256 (ttp) cc_final: 0.7735 (tmm) REVERT: G 41 GLU cc_start: 0.7020 (tp30) cc_final: 0.6694 (mm-30) outliers start: 54 outliers final: 22 residues processed: 212 average time/residue: 1.3520 time to fit residues: 305.2130 Evaluate side-chains 220 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 185 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 20 MET 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 E residue 167 SER Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 51 THR 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 28 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 C residue 212 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 24 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.0870 chunk 113 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 0.0060 chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 138 GLN E 214 ASN C 138 GLN B 168 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10060 Z= 0.164 Angle : 0.479 7.227 13549 Z= 0.247 Chirality : 0.036 0.129 1596 Planarity : 0.004 0.055 1729 Dihedral : 4.531 50.086 1382 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.41 % Allowed : 19.48 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.23), residues: 1298 helix: 2.38 (0.15), residues: 1101 sheet: None (None), residues: 0 loop : 0.22 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 18 HIS 0.001 0.000 HIS D 136 PHE 0.029 0.001 PHE A 44 TYR 0.005 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 236 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 190 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.2924 (OUTLIER) cc_final: 0.2246 (mt) REVERT: A 32 VAL cc_start: 0.7457 (OUTLIER) cc_final: 0.7116 (t) REVERT: A 48 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6490 (mpp) REVERT: A 52 MET cc_start: 0.7107 (mmt) cc_final: 0.6895 (mmm) REVERT: A 64 LYS cc_start: 0.6472 (mttt) cc_final: 0.5997 (mtpt) REVERT: A 69 LYS cc_start: 0.6246 (tptp) cc_final: 0.5740 (mppt) REVERT: A 98 MET cc_start: 0.4764 (OUTLIER) cc_final: 0.4549 (ttp) REVERT: A 195 MET cc_start: 0.8075 (mtp) cc_final: 0.7765 (mmm) REVERT: A 208 ARG cc_start: 0.6894 (ttm110) cc_final: 0.6591 (ttp80) REVERT: E 28 MET cc_start: 0.4645 (ptt) cc_final: 0.4322 (ptt) REVERT: E 52 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.7001 (tpt) REVERT: E 67 MET cc_start: 0.7127 (ptp) cc_final: 0.6640 (ptt) REVERT: E 155 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8276 (tmm) REVERT: E 165 MET cc_start: 0.8412 (mtp) cc_final: 0.8024 (mtp) REVERT: E 173 LYS cc_start: 0.7973 (mmtt) cc_final: 0.7202 (mmtt) REVERT: E 219 MET cc_start: 0.4749 (ttp) cc_final: 0.3980 (tpt) REVERT: D 49 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7165 (mttt) REVERT: D 64 LYS cc_start: 0.7543 (ptpp) cc_final: 0.6156 (pptt) REVERT: D 83 MET cc_start: 0.5792 (OUTLIER) cc_final: 0.5170 (mpp) REVERT: D 153 MET cc_start: 0.8366 (mmm) cc_final: 0.8112 (tpp) REVERT: D 173 LYS cc_start: 0.7522 (mttt) cc_final: 0.7218 (mttp) REVERT: C 64 LYS cc_start: 0.6513 (mmtm) cc_final: 0.6191 (mttm) REVERT: C 67 MET cc_start: 0.6898 (mtp) cc_final: 0.6148 (mmp) REVERT: C 135 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.7011 (mtm-85) REVERT: C 179 MET cc_start: 0.8014 (tpt) cc_final: 0.7605 (tpp) REVERT: C 186 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8382 (m) REVERT: C 208 ARG cc_start: 0.7607 (ttp80) cc_final: 0.6421 (ttp-110) REVERT: B 36 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7748 (mp) REVERT: B 52 MET cc_start: 0.7569 (mmm) cc_final: 0.7207 (mmt) REVERT: B 67 MET cc_start: 0.7032 (ptp) cc_final: 0.6794 (ptm) REVERT: B 71 ASP cc_start: 0.6114 (m-30) cc_final: 0.5690 (t70) REVERT: B 117 ASP cc_start: 0.6128 (OUTLIER) cc_final: 0.5269 (t70) REVERT: B 173 LYS cc_start: 0.6985 (pttp) cc_final: 0.6637 (mmpt) REVERT: F 25 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7894 (tp) REVERT: F 41 GLU cc_start: 0.6270 (mm-30) cc_final: 0.5871 (pt0) REVERT: G 30 MET cc_start: 0.8217 (ttp) cc_final: 0.7700 (tmm) REVERT: G 41 GLU cc_start: 0.6996 (tp30) cc_final: 0.6725 (mm-30) outliers start: 46 outliers final: 11 residues processed: 208 average time/residue: 1.3842 time to fit residues: 306.3208 Evaluate side-chains 209 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 186 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 98 MET 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 49 LYS Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 71 ASP 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 117 ASP Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain G residue 24 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 125 optimal weight: 0.3980 chunk 78 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 57 optimal weight: 0.1980 chunk 77 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN B 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10060 Z= 0.167 Angle : 0.477 7.846 13549 Z= 0.246 Chirality : 0.036 0.116 1596 Planarity : 0.004 0.053 1729 Dihedral : 4.474 49.869 1382 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.84 % Allowed : 19.77 % 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: 3.16 (0.23), residues: 1298 helix: 2.38 (0.15), residues: 1116 sheet: None (None), residues: 0 loop : 0.28 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 18 HIS 0.001 0.000 HIS D 136 PHE 0.015 0.001 PHE F 39 TYR 0.005 0.001 TYR E 241 ARG 0.007 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 227 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 187 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.2828 (OUTLIER) cc_final: 0.2243 (mt) REVERT: A 32 VAL cc_start: 0.7503 (OUTLIER) cc_final: 0.7166 (t) REVERT: A 48 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6547 (mpp) REVERT: A 52 MET cc_start: 0.7137 (mmt) cc_final: 0.6860 (mmm) REVERT: A 64 LYS cc_start: 0.6463 (mttt) cc_final: 0.6006 (mtpt) REVERT: A 69 LYS cc_start: 0.6292 (tptp) cc_final: 0.5793 (mppt) REVERT: A 195 MET cc_start: 0.8083 (mtp) cc_final: 0.7767 (mmm) REVERT: A 208 ARG cc_start: 0.6876 (ttm110) cc_final: 0.6575 (ttp80) REVERT: E 28 MET cc_start: 0.4544 (ptt) cc_final: 0.4224 (ptt) REVERT: E 52 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6998 (tpt) REVERT: E 59 THR cc_start: 0.7794 (m) cc_final: 0.7338 (p) REVERT: E 67 MET cc_start: 0.7117 (ptp) cc_final: 0.6637 (ptt) REVERT: E 155 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8266 (tmm) REVERT: E 165 MET cc_start: 0.8410 (mtp) cc_final: 0.7985 (mtp) REVERT: E 173 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7195 (mmtt) REVERT: E 219 MET cc_start: 0.4724 (ttp) cc_final: 0.4041 (tpt) REVERT: D 49 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7140 (mttt) REVERT: D 64 LYS cc_start: 0.7517 (ptpp) cc_final: 0.6180 (pptt) REVERT: D 83 MET cc_start: 0.5748 (OUTLIER) cc_final: 0.5196 (mpp) REVERT: D 128 ASP cc_start: 0.5818 (OUTLIER) cc_final: 0.5597 (m-30) REVERT: D 153 MET cc_start: 0.8366 (mmm) cc_final: 0.8111 (tpp) REVERT: D 173 LYS cc_start: 0.7511 (mttt) cc_final: 0.7210 (mttp) REVERT: C 64 LYS cc_start: 0.6504 (mmtm) cc_final: 0.6170 (mttm) REVERT: C 67 MET cc_start: 0.6916 (mtp) cc_final: 0.6171 (mmp) REVERT: C 131 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6329 (mm) REVERT: C 135 ARG cc_start: 0.7295 (mtm-85) cc_final: 0.7020 (mtm-85) REVERT: C 179 MET cc_start: 0.7970 (tpt) cc_final: 0.7544 (tpp) REVERT: C 186 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8407 (m) REVERT: C 208 ARG cc_start: 0.7609 (ttp80) cc_final: 0.6423 (ttp-110) REVERT: B 36 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7787 (mp) REVERT: B 52 MET cc_start: 0.7538 (mmm) cc_final: 0.7178 (mmt) REVERT: B 67 MET cc_start: 0.7037 (ptp) cc_final: 0.6797 (ptm) REVERT: B 71 ASP cc_start: 0.6093 (m-30) cc_final: 0.5678 (t70) REVERT: B 117 ASP cc_start: 0.6122 (OUTLIER) cc_final: 0.5249 (t70) REVERT: B 173 LYS cc_start: 0.7033 (pttp) cc_final: 0.6789 (mtmm) REVERT: F 25 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7892 (tp) REVERT: F 41 GLU cc_start: 0.6230 (mm-30) cc_final: 0.5958 (pt0) REVERT: F 44 VAL cc_start: 0.7394 (t) cc_final: 0.7162 (m) REVERT: G 30 MET cc_start: 0.8272 (ttp) cc_final: 0.7741 (tmm) REVERT: G 41 GLU cc_start: 0.6873 (tp30) cc_final: 0.6614 (mm-30) outliers start: 40 outliers final: 16 residues processed: 208 average time/residue: 1.3765 time to fit residues: 304.4892 Evaluate side-chains 215 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 186 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 A residue 230 ASN Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 71 ASP 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 117 ASP 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 F residue 55 LYS Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 27 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.2980 chunk 74 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 120 optimal weight: 0.0060 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN B 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10060 Z= 0.174 Angle : 0.491 8.239 13549 Z= 0.251 Chirality : 0.036 0.116 1596 Planarity : 0.004 0.054 1729 Dihedral : 4.465 49.766 1382 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.93 % Allowed : 19.96 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.18 (0.23), residues: 1298 helix: 2.39 (0.15), residues: 1116 sheet: None (None), residues: 0 loop : 0.27 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 18 HIS 0.001 0.000 HIS D 136 PHE 0.028 0.001 PHE A 44 TYR 0.005 0.001 TYR C 241 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 225 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 184 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.2825 (OUTLIER) cc_final: 0.2237 (mt) REVERT: A 18 MET cc_start: 0.3102 (tpt) cc_final: 0.2423 (tpt) REVERT: A 32 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7166 (t) REVERT: A 48 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6512 (mpp) REVERT: A 52 MET cc_start: 0.7158 (mmt) cc_final: 0.6885 (mmm) REVERT: A 64 LYS cc_start: 0.6498 (mttt) cc_final: 0.6004 (mtpt) REVERT: A 69 LYS cc_start: 0.6297 (tptp) cc_final: 0.5708 (mppt) REVERT: A 195 MET cc_start: 0.8095 (mtp) cc_final: 0.7769 (mmm) REVERT: A 208 ARG cc_start: 0.6933 (ttm110) cc_final: 0.6635 (ttp80) REVERT: E 28 MET cc_start: 0.4600 (ptt) cc_final: 0.4287 (ptt) REVERT: E 52 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6994 (tpt) REVERT: E 59 THR cc_start: 0.7792 (m) cc_final: 0.7346 (p) REVERT: E 67 MET cc_start: 0.7122 (ptp) cc_final: 0.6649 (ptt) REVERT: E 155 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8270 (tmm) REVERT: E 165 MET cc_start: 0.8401 (mtp) cc_final: 0.8002 (mtp) REVERT: E 173 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7176 (mmtt) REVERT: E 219 MET cc_start: 0.4675 (ttp) cc_final: 0.4003 (tpt) REVERT: D 49 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7143 (mttt) REVERT: D 64 LYS cc_start: 0.7483 (ptpp) cc_final: 0.6179 (pptt) REVERT: D 83 MET cc_start: 0.5745 (OUTLIER) cc_final: 0.5191 (mpp) REVERT: D 128 ASP cc_start: 0.5840 (OUTLIER) cc_final: 0.5611 (m-30) REVERT: D 153 MET cc_start: 0.8365 (mmm) cc_final: 0.8113 (tpp) REVERT: D 173 LYS cc_start: 0.7515 (mttt) cc_final: 0.7220 (mttp) REVERT: C 64 LYS cc_start: 0.6507 (mmtm) cc_final: 0.6170 (mttm) REVERT: C 67 MET cc_start: 0.6939 (mtp) cc_final: 0.6176 (mmp) REVERT: C 131 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6334 (mm) REVERT: C 135 ARG cc_start: 0.7302 (mtm-85) cc_final: 0.7017 (mtm-85) REVERT: C 179 MET cc_start: 0.7979 (tpt) cc_final: 0.7555 (tpp) REVERT: C 186 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8410 (m) REVERT: C 208 ARG cc_start: 0.7605 (ttp80) cc_final: 0.6416 (ttp-110) REVERT: B 36 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7791 (mp) REVERT: B 52 MET cc_start: 0.7562 (mmm) cc_final: 0.7214 (mmt) REVERT: B 67 MET cc_start: 0.7047 (ptp) cc_final: 0.6813 (ptm) REVERT: B 71 ASP cc_start: 0.6093 (m-30) cc_final: 0.5670 (t70) REVERT: B 117 ASP cc_start: 0.6134 (OUTLIER) cc_final: 0.5267 (t70) REVERT: B 173 LYS cc_start: 0.7044 (pttp) cc_final: 0.6801 (mtmm) REVERT: F 25 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7896 (tp) REVERT: F 41 GLU cc_start: 0.6193 (mm-30) cc_final: 0.5820 (pt0) REVERT: F 44 VAL cc_start: 0.7435 (t) cc_final: 0.7176 (m) REVERT: F 46 LYS cc_start: 0.7853 (mtpt) cc_final: 0.6604 (tmtt) REVERT: G 30 MET cc_start: 0.8270 (ttp) cc_final: 0.7678 (tmm) REVERT: G 41 GLU cc_start: 0.6850 (tp30) cc_final: 0.5204 (pm20) outliers start: 41 outliers final: 14 residues processed: 204 average time/residue: 1.3539 time to fit residues: 293.7269 Evaluate side-chains 207 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 155 MET Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 71 ASP 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 117 ASP 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 F residue 55 LYS Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 27 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 120 optimal weight: 0.0470 chunk 70 optimal weight: 0.0470 chunk 50 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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: 0.7628 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10060 Z= 0.170 Angle : 0.489 7.888 13549 Z= 0.251 Chirality : 0.036 0.125 1596 Planarity : 0.004 0.053 1729 Dihedral : 4.442 49.463 1382 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.45 % Allowed : 20.35 % Favored : 76.20 % 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: 3.22 (0.23), residues: 1298 helix: 2.43 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : 0.25 (0.47), residues: 183 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 C 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 218 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 182 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.2819 (OUTLIER) cc_final: 0.2248 (mt) REVERT: A 18 MET cc_start: 0.3346 (tpt) cc_final: 0.2603 (tpt) REVERT: A 32 VAL cc_start: 0.7457 (OUTLIER) cc_final: 0.7129 (t) REVERT: A 48 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6560 (mpp) REVERT: A 52 MET cc_start: 0.7137 (mmt) cc_final: 0.6857 (mmm) REVERT: A 64 LYS cc_start: 0.6504 (mttt) cc_final: 0.6032 (mtpt) REVERT: A 69 LYS cc_start: 0.6165 (tptp) cc_final: 0.5700 (mppt) REVERT: A 195 MET cc_start: 0.8088 (mtp) cc_final: 0.7760 (mmm) REVERT: A 208 ARG cc_start: 0.6882 (ttm110) cc_final: 0.6595 (ttp80) REVERT: E 28 MET cc_start: 0.4605 (ptt) cc_final: 0.4273 (ptt) REVERT: E 59 THR cc_start: 0.7819 (m) cc_final: 0.7400 (p) REVERT: E 67 MET cc_start: 0.7128 (ptp) cc_final: 0.6650 (ptt) REVERT: E 155 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8269 (tmm) REVERT: E 165 MET cc_start: 0.8396 (mtp) cc_final: 0.7996 (mtp) REVERT: E 173 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7190 (mmtt) REVERT: E 219 MET cc_start: 0.4742 (ttp) cc_final: 0.4010 (tpt) REVERT: D 49 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7165 (mttt) REVERT: D 64 LYS cc_start: 0.7450 (ptpp) cc_final: 0.6105 (pptt) REVERT: D 83 MET cc_start: 0.5762 (OUTLIER) cc_final: 0.5206 (mpp) REVERT: D 128 ASP cc_start: 0.5823 (OUTLIER) cc_final: 0.5584 (m-30) REVERT: D 153 MET cc_start: 0.8363 (mmm) cc_final: 0.8113 (tpp) REVERT: D 173 LYS cc_start: 0.7487 (mttt) cc_final: 0.7206 (mttp) REVERT: C 64 LYS cc_start: 0.6525 (mmtm) cc_final: 0.6189 (mttm) REVERT: C 131 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6345 (mm) REVERT: C 135 ARG cc_start: 0.7292 (mtm-85) cc_final: 0.7016 (mtm-85) REVERT: C 179 MET cc_start: 0.7977 (tpt) cc_final: 0.7552 (tpp) REVERT: C 186 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8408 (m) REVERT: C 208 ARG cc_start: 0.7649 (ttp80) cc_final: 0.6465 (ttp-110) REVERT: B 36 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7852 (mp) REVERT: B 52 MET cc_start: 0.7564 (mmm) cc_final: 0.7218 (mmt) REVERT: B 67 MET cc_start: 0.7046 (ptp) cc_final: 0.6814 (ptm) REVERT: B 71 ASP cc_start: 0.6124 (m-30) cc_final: 0.5716 (t70) REVERT: B 117 ASP cc_start: 0.6129 (OUTLIER) cc_final: 0.5267 (t70) REVERT: B 173 LYS cc_start: 0.7019 (pttp) cc_final: 0.6781 (mtmm) REVERT: F 25 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7886 (tp) REVERT: F 41 GLU cc_start: 0.6131 (mm-30) cc_final: 0.5764 (pt0) REVERT: F 44 VAL cc_start: 0.7405 (t) cc_final: 0.7138 (m) REVERT: F 46 LYS cc_start: 0.7835 (mtpt) cc_final: 0.6610 (tmtt) REVERT: G 30 MET cc_start: 0.8273 (ttp) cc_final: 0.7676 (tmm) REVERT: G 41 GLU cc_start: 0.6824 (tp30) cc_final: 0.5203 (pm20) outliers start: 36 outliers final: 16 residues processed: 201 average time/residue: 1.3559 time to fit residues: 289.8442 Evaluate side-chains 208 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain A residue 230 ASN 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 51 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 71 ASP 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 117 ASP 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 F residue 55 LYS Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 27 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 chunk 85 optimal weight: 5.9990 chunk 129 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 81 optimal weight: 0.3980 chunk 109 optimal weight: 0.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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: 0.7628 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10060 Z= 0.172 Angle : 0.495 7.824 13549 Z= 0.253 Chirality : 0.036 0.157 1596 Planarity : 0.004 0.053 1729 Dihedral : 4.440 49.309 1382 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.17 % Allowed : 20.92 % Favored : 75.91 % 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: 3.22 (0.23), residues: 1298 helix: 2.43 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : 0.27 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 18 HIS 0.001 0.000 HIS D 136 PHE 0.030 0.001 PHE A 44 TYR 0.005 0.001 TYR C 241 ARG 0.009 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 fitting. rotamer outliers: 33 poor density : 179 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.3001 (OUTLIER) cc_final: 0.2402 (mt) REVERT: A 32 VAL cc_start: 0.7459 (OUTLIER) cc_final: 0.7129 (t) REVERT: A 48 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6560 (mpp) REVERT: A 52 MET cc_start: 0.7146 (mmt) cc_final: 0.6866 (mmm) REVERT: A 64 LYS cc_start: 0.6510 (mttt) cc_final: 0.6038 (mtpt) REVERT: A 69 LYS cc_start: 0.6147 (tptp) cc_final: 0.5710 (mppt) REVERT: A 195 MET cc_start: 0.8079 (mtp) cc_final: 0.7749 (mmm) REVERT: A 208 ARG cc_start: 0.6927 (ttm110) cc_final: 0.6643 (ttp80) REVERT: E 28 MET cc_start: 0.4606 (ptt) cc_final: 0.4283 (ptt) REVERT: E 59 THR cc_start: 0.7819 (m) cc_final: 0.7406 (p) REVERT: E 64 LYS cc_start: 0.6923 (mttm) cc_final: 0.6170 (tmtt) REVERT: E 67 MET cc_start: 0.7170 (ptp) cc_final: 0.6709 (ptt) REVERT: E 155 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8267 (tmm) REVERT: E 165 MET cc_start: 0.8394 (mtp) cc_final: 0.7997 (mtp) REVERT: E 173 LYS cc_start: 0.7992 (mmtt) cc_final: 0.7192 (mmtt) REVERT: E 219 MET cc_start: 0.4749 (ttp) cc_final: 0.4055 (tpt) REVERT: D 49 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7144 (mttt) REVERT: D 64 LYS cc_start: 0.7380 (ptpp) cc_final: 0.6346 (ttpp) REVERT: D 83 MET cc_start: 0.5766 (OUTLIER) cc_final: 0.5206 (mpp) REVERT: D 128 ASP cc_start: 0.5818 (OUTLIER) cc_final: 0.5581 (m-30) REVERT: C 64 LYS cc_start: 0.6498 (mmtm) cc_final: 0.6185 (mttm) REVERT: C 67 MET cc_start: 0.7045 (mtp) cc_final: 0.6134 (mmp) REVERT: C 131 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6351 (mm) REVERT: C 135 ARG cc_start: 0.7294 (mtm-85) cc_final: 0.7009 (mtm-85) REVERT: C 179 MET cc_start: 0.7976 (tpt) cc_final: 0.7554 (tpp) REVERT: C 186 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8412 (m) REVERT: C 208 ARG cc_start: 0.7648 (ttp80) cc_final: 0.6463 (ttp-110) REVERT: B 36 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7864 (mp) REVERT: B 52 MET cc_start: 0.7544 (mmm) cc_final: 0.7190 (mmt) REVERT: B 67 MET cc_start: 0.7046 (ptp) cc_final: 0.6812 (ptm) REVERT: B 71 ASP cc_start: 0.6123 (m-30) cc_final: 0.5712 (t70) REVERT: B 117 ASP cc_start: 0.6161 (OUTLIER) cc_final: 0.5350 (t70) REVERT: B 173 LYS cc_start: 0.7019 (pttp) cc_final: 0.6784 (mtmm) REVERT: F 25 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7892 (tp) REVERT: F 41 GLU cc_start: 0.6118 (mm-30) cc_final: 0.5727 (pt0) REVERT: F 44 VAL cc_start: 0.7431 (t) cc_final: 0.7164 (m) REVERT: F 46 LYS cc_start: 0.7823 (mtpt) cc_final: 0.6606 (tmtt) REVERT: G 30 MET cc_start: 0.8262 (ttp) cc_final: 0.7664 (tmm) REVERT: G 41 GLU cc_start: 0.6817 (tp30) cc_final: 0.5196 (pm20) outliers start: 33 outliers final: 16 residues processed: 198 average time/residue: 1.3573 time to fit residues: 286.0679 Evaluate side-chains 207 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 179 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain A residue 230 ASN 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 51 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain C residue 18 MET Chi-restraints excluded: chain C residue 71 ASP 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 B residue 26 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 117 ASP 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 F residue 55 LYS Chi-restraints excluded: chain G residue 24 ASP Chi-restraints excluded: chain G residue 27 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.235691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157540 restraints weight = 8380.139| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.69 r_work: 0.3564 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10060 Z= 0.227 Angle : 0.533 8.222 13549 Z= 0.274 Chirality : 0.037 0.213 1596 Planarity : 0.005 0.056 1729 Dihedral : 4.566 51.107 1382 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.17 % Allowed : 20.92 % Favored : 75.91 % 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: 3.00 (0.23), residues: 1298 helix: 2.28 (0.15), residues: 1114 sheet: None (None), residues: 0 loop : 0.23 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 18 HIS 0.001 0.000 HIS D 136 PHE 0.016 0.002 PHE F 39 TYR 0.008 0.001 TYR C 241 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: 5077.23 seconds wall clock time: 90 minutes 15.07 seconds (5415.07 seconds total)