Starting phenix.real_space_refine on Mon Dec 30 09:16:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ip3_35630/12_2024/8ip3_35630.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ip3_35630/12_2024/8ip3_35630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ip3_35630/12_2024/8ip3_35630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ip3_35630/12_2024/8ip3_35630.map" model { file = "/net/cci-nas-00/data/ceres_data/8ip3_35630/12_2024/8ip3_35630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ip3_35630/12_2024/8ip3_35630.cif" } resolution = 2.6 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= 0.027 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: 6 Type Number sf(0) Gaussians Mg 12 5.21 5 S 65 5.16 5 Cl 1 4.86 5 C 8275 2.51 5 N 2155 2.21 5 O 2360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12868 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2571 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 310} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CL': 1, ' MG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 6.24, per 1000 atoms: 0.48 Number of scatterers: 12868 At special positions: 0 Unit cell: (108.81, 106.95, 141.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 65 16.00 Mg 12 11.99 O 2360 8.00 N 2155 7.00 C 8275 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.7 seconds 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3040 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 72.4% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.564A pdb=" N ARG A 119 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 173 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 183 through 219 removed outlier: 3.625A pdb=" N ARG A 187 " --> pdb=" O PRO A 183 " (cutoff:3.500A) Proline residue: A 209 - end of helix Processing helix chain 'A' and resid 227 through 261 removed outlier: 4.050A pdb=" N GLU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.516A pdb=" N LEU A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.932A pdb=" N ASP A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 removed outlier: 4.099A pdb=" N LYS A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 359 Processing helix chain 'A' and resid 371 through 401 removed outlier: 4.425A pdb=" N TRP A 375 " --> pdb=" O HIS A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 114 through 119 removed outlier: 3.565A pdb=" N ARG B 119 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 173 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 183 through 219 removed outlier: 3.625A pdb=" N ARG B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Proline residue: B 209 - end of helix Processing helix chain 'B' and resid 227 through 261 removed outlier: 4.051A pdb=" N GLU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 269 removed outlier: 3.517A pdb=" N LEU B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 removed outlier: 3.932A pdb=" N ASP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 283 removed outlier: 4.099A pdb=" N LYS B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 359 Processing helix chain 'B' and resid 371 through 401 removed outlier: 4.424A pdb=" N TRP B 375 " --> pdb=" O HIS B 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 114 through 119 removed outlier: 3.564A pdb=" N ARG C 119 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 173 Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 183 through 219 removed outlier: 3.625A pdb=" N ARG C 187 " --> pdb=" O PRO C 183 " (cutoff:3.500A) Proline residue: C 209 - end of helix Processing helix chain 'C' and resid 227 through 261 removed outlier: 4.051A pdb=" N GLU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 269 removed outlier: 3.516A pdb=" N LEU C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.931A pdb=" N ASP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 283 removed outlier: 4.099A pdb=" N LYS C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 359 Processing helix chain 'C' and resid 371 through 401 removed outlier: 4.425A pdb=" N TRP C 375 " --> pdb=" O HIS C 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.565A pdb=" N ARG D 119 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 173 Proline residue: D 168 - end of helix Processing helix chain 'D' and resid 183 through 219 removed outlier: 3.625A pdb=" N ARG D 187 " --> pdb=" O PRO D 183 " (cutoff:3.500A) Proline residue: D 209 - end of helix Processing helix chain 'D' and resid 227 through 261 removed outlier: 4.050A pdb=" N GLU D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 removed outlier: 3.517A pdb=" N LEU D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.932A pdb=" N ASP D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 283 removed outlier: 4.099A pdb=" N LYS D 281 " --> pdb=" O GLN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 359 Processing helix chain 'D' and resid 371 through 401 removed outlier: 4.425A pdb=" N TRP D 375 " --> pdb=" O HIS D 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 114 through 119 removed outlier: 3.565A pdb=" N ARG E 119 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 173 Proline residue: E 168 - end of helix Processing helix chain 'E' and resid 183 through 219 removed outlier: 3.625A pdb=" N ARG E 187 " --> pdb=" O PRO E 183 " (cutoff:3.500A) Proline residue: E 209 - end of helix Processing helix chain 'E' and resid 227 through 261 removed outlier: 4.051A pdb=" N GLU E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 269 removed outlier: 3.517A pdb=" N LEU E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS E 269 " --> pdb=" O LEU E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 removed outlier: 3.932A pdb=" N ASP E 275 " --> pdb=" O SER E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 283 removed outlier: 4.099A pdb=" N LYS E 281 " --> pdb=" O GLN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 359 Processing helix chain 'E' and resid 371 through 401 removed outlier: 4.424A pdb=" N TRP E 375 " --> pdb=" O HIS E 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 103 removed outlier: 4.191A pdb=" N LYS A 141 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 103 removed outlier: 4.192A pdb=" N LYS B 141 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 103 removed outlier: 4.192A pdb=" N LYS C 141 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 97 through 103 removed outlier: 4.192A pdb=" N LYS D 141 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 103 removed outlier: 4.192A pdb=" N LYS E 141 " --> pdb=" O LEU E 152 " (cutoff:3.500A) 1015 hydrogen bonds defined for protein. 2970 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: 3.95 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4210 1.34 - 1.46: 2437 1.46 - 1.58: 6318 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 13085 Sorted by residual: bond pdb=" C SER B 348 " pdb=" O SER B 348 " ideal model delta sigma weight residual 1.237 1.245 -0.008 1.17e-02 7.31e+03 5.01e-01 bond pdb=" C SER E 348 " pdb=" O SER E 348 " ideal model delta sigma weight residual 1.237 1.245 -0.008 1.17e-02 7.31e+03 4.74e-01 bond pdb=" CA LEU D 354 " pdb=" C LEU D 354 " ideal model delta sigma weight residual 1.523 1.515 0.008 1.30e-02 5.92e+03 4.19e-01 bond pdb=" CA LEU C 354 " pdb=" C LEU C 354 " ideal model delta sigma weight residual 1.523 1.515 0.008 1.30e-02 5.92e+03 4.11e-01 bond pdb=" C SER D 348 " pdb=" O SER D 348 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.17e-02 7.31e+03 4.03e-01 ... (remaining 13080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 17215 1.04 - 2.09: 375 2.09 - 3.13: 55 3.13 - 4.17: 20 4.17 - 5.21: 20 Bond angle restraints: 17685 Sorted by residual: angle pdb=" C LEU E 351 " pdb=" N PHE E 352 " pdb=" CA PHE E 352 " ideal model delta sigma weight residual 121.14 117.47 3.67 1.75e+00 3.27e-01 4.41e+00 angle pdb=" C LEU C 351 " pdb=" N PHE C 352 " pdb=" CA PHE C 352 " ideal model delta sigma weight residual 121.14 117.47 3.67 1.75e+00 3.27e-01 4.39e+00 angle pdb=" C LEU B 351 " pdb=" N PHE B 352 " pdb=" CA PHE B 352 " ideal model delta sigma weight residual 121.14 117.47 3.67 1.75e+00 3.27e-01 4.39e+00 angle pdb=" C LEU A 351 " pdb=" N PHE A 352 " pdb=" CA PHE A 352 " ideal model delta sigma weight residual 121.14 117.47 3.67 1.75e+00 3.27e-01 4.39e+00 angle pdb=" C LEU D 351 " pdb=" N PHE D 352 " pdb=" CA PHE D 352 " ideal model delta sigma weight residual 121.14 117.48 3.66 1.75e+00 3.27e-01 4.37e+00 ... (remaining 17680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 7428 17.51 - 35.03: 462 35.03 - 52.54: 35 52.54 - 70.05: 5 70.05 - 87.57: 5 Dihedral angle restraints: 7935 sinusoidal: 3270 harmonic: 4665 Sorted by residual: dihedral pdb=" CB GLU E 147 " pdb=" CG GLU E 147 " pdb=" CD GLU E 147 " pdb=" OE1 GLU E 147 " ideal model delta sinusoidal sigma weight residual 0.00 87.57 -87.57 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU D 147 " pdb=" CG GLU D 147 " pdb=" CD GLU D 147 " pdb=" OE1 GLU D 147 " ideal model delta sinusoidal sigma weight residual 0.00 87.54 -87.54 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU B 147 " pdb=" CG GLU B 147 " pdb=" CD GLU B 147 " pdb=" OE1 GLU B 147 " ideal model delta sinusoidal sigma weight residual 0.00 87.54 -87.54 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 7932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1379 0.029 - 0.058: 420 0.058 - 0.086: 156 0.086 - 0.115: 75 0.115 - 0.144: 20 Chirality restraints: 2050 Sorted by residual: chirality pdb=" CA LEU A 167 " pdb=" N LEU A 167 " pdb=" C LEU A 167 " pdb=" CB LEU A 167 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA LEU C 167 " pdb=" N LEU C 167 " pdb=" C LEU C 167 " pdb=" CB LEU C 167 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA LEU B 167 " pdb=" N LEU B 167 " pdb=" C LEU B 167 " pdb=" CB LEU B 167 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 2047 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 163 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C LEU B 163 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU B 163 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE B 164 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 163 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C LEU E 163 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU E 163 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE E 164 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 163 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C LEU A 163 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU A 163 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 164 " 0.012 2.00e-02 2.50e+03 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2582 2.78 - 3.31: 13000 3.31 - 3.84: 21592 3.84 - 4.37: 25684 4.37 - 4.90: 45039 Nonbonded interactions: 107897 Sorted by model distance: nonbonded pdb=" OG SER D 99 " pdb=" OH TYR D 154 " model vdw 2.255 3.040 nonbonded pdb=" OG SER E 99 " pdb=" OH TYR E 154 " model vdw 2.255 3.040 nonbonded pdb=" OG SER C 99 " pdb=" OH TYR C 154 " model vdw 2.255 3.040 nonbonded pdb=" OG SER B 99 " pdb=" OH TYR B 154 " model vdw 2.255 3.040 nonbonded pdb=" OG SER A 99 " pdb=" OH TYR A 154 " model vdw 2.256 3.040 ... (remaining 107892 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 83 through 401 or resid 502)) selection = (chain 'B' and (resid 83 through 401 or resid 502)) selection = (chain 'C' and (resid 83 through 401 or resid 502)) selection = (chain 'D' and (resid 83 through 401 or resid 502)) selection = (chain 'E' and (resid 83 through 401 or resid 502)) } 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=1.00 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: 1.110 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: 0.000 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.990 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 0.002 0.018 13085 Z= 0.153 Angle : 0.425 5.214 17685 Z= 0.224 Chirality : 0.037 0.144 2050 Planarity : 0.003 0.029 2235 Dihedral : 10.758 87.566 4895 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 3.79 (0.21), residues: 1585 helix: 3.32 (0.15), residues: 1040 sheet: 2.16 (0.38), residues: 145 loop : 0.33 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 162 HIS 0.001 0.000 HIS C 223 PHE 0.016 0.001 PHE D 352 TYR 0.012 0.001 TYR E 299 ARG 0.001 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.652 Fit side-chains REVERT: A 383 MET cc_start: 0.6980 (mmp) cc_final: 0.6550 (mtp) REVERT: C 383 MET cc_start: 0.6789 (mmp) cc_final: 0.6236 (mtm) REVERT: D 383 MET cc_start: 0.6884 (mmp) cc_final: 0.6458 (mtp) REVERT: E 383 MET cc_start: 0.7061 (mmp) cc_final: 0.6482 (mtp) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 1.3729 time to fit residues: 310.3294 Evaluate side-chains 152 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 0.0870 chunk 40 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 121 GLN E 362 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13085 Z= 0.356 Angle : 0.536 8.016 17685 Z= 0.278 Chirality : 0.042 0.216 2050 Planarity : 0.004 0.032 2235 Dihedral : 4.003 14.119 1720 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.99 % Allowed : 6.71 % Favored : 92.30 % 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: 3.50 (0.21), residues: 1585 helix: 3.16 (0.15), residues: 1020 sheet: 2.05 (0.39), residues: 145 loop : 0.19 (0.35), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 196 HIS 0.003 0.001 HIS C 122 PHE 0.023 0.002 PHE A 395 TYR 0.025 0.002 TYR C 299 ARG 0.004 0.000 ARG B 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 1.704 Fit side-chains REVERT: A 94 GLN cc_start: 0.8149 (mp10) cc_final: 0.7871 (mp10) REVERT: A 383 MET cc_start: 0.7053 (mmp) cc_final: 0.6658 (mtp) REVERT: C 350 SER cc_start: 0.8445 (t) cc_final: 0.8194 (m) REVERT: C 383 MET cc_start: 0.6990 (mmp) cc_final: 0.6563 (mtm) REVERT: D 350 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8528 (p) REVERT: D 383 MET cc_start: 0.6944 (mmp) cc_final: 0.6565 (mtp) REVERT: E 94 GLN cc_start: 0.8194 (mp10) cc_final: 0.7791 (mp10) REVERT: E 350 SER cc_start: 0.8579 (t) cc_final: 0.8197 (p) REVERT: E 355 MET cc_start: 0.8375 (ttm) cc_final: 0.8065 (ttm) REVERT: E 362 ASN cc_start: 0.8193 (m110) cc_final: 0.7983 (m-40) REVERT: E 383 MET cc_start: 0.7115 (mmp) cc_final: 0.6568 (mtp) outliers start: 14 outliers final: 5 residues processed: 160 average time/residue: 1.2964 time to fit residues: 227.1224 Evaluate side-chains 145 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 355 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 362 ASN E 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13085 Z= 0.250 Angle : 0.480 8.830 17685 Z= 0.252 Chirality : 0.040 0.214 2050 Planarity : 0.004 0.036 2235 Dihedral : 3.925 14.246 1720 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.70 % Allowed : 7.14 % Favored : 91.17 % 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: 3.50 (0.21), residues: 1585 helix: 2.92 (0.15), residues: 1050 sheet: 2.09 (0.40), residues: 145 loop : 0.71 (0.36), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 375 HIS 0.002 0.000 HIS C 122 PHE 0.019 0.002 PHE A 352 TYR 0.018 0.002 TYR C 299 ARG 0.003 0.000 ARG B 165 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.543 Fit side-chains REVERT: A 94 GLN cc_start: 0.8113 (mp10) cc_final: 0.7833 (mp10) REVERT: A 359 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.8019 (t80) REVERT: A 383 MET cc_start: 0.6862 (mmp) cc_final: 0.6513 (mtp) REVERT: B 355 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8184 (ttp) REVERT: B 359 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.8045 (t80) REVERT: B 383 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6427 (mpp) REVERT: C 350 SER cc_start: 0.8385 (t) cc_final: 0.8183 (m) REVERT: C 383 MET cc_start: 0.6956 (mmp) cc_final: 0.6528 (mtm) REVERT: D 359 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7940 (t80) REVERT: D 383 MET cc_start: 0.6894 (mmp) cc_final: 0.6537 (mtp) REVERT: D 391 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6588 (ttp-170) REVERT: E 94 GLN cc_start: 0.8156 (mp10) cc_final: 0.7830 (mp10) REVERT: E 350 SER cc_start: 0.8570 (t) cc_final: 0.8214 (p) REVERT: E 355 MET cc_start: 0.8373 (ttm) cc_final: 0.8069 (ttm) REVERT: E 383 MET cc_start: 0.7018 (mmp) cc_final: 0.6506 (mtp) outliers start: 24 outliers final: 7 residues processed: 164 average time/residue: 1.3446 time to fit residues: 241.0765 Evaluate side-chains 161 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN E 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 13085 Z= 0.379 Angle : 0.535 8.684 17685 Z= 0.278 Chirality : 0.042 0.218 2050 Planarity : 0.004 0.037 2235 Dihedral : 4.101 14.597 1720 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.84 % Allowed : 8.62 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.21), residues: 1585 helix: 2.90 (0.15), residues: 1040 sheet: 2.02 (0.40), residues: 145 loop : -0.01 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 375 HIS 0.002 0.001 HIS C 122 PHE 0.020 0.002 PHE D 352 TYR 0.026 0.002 TYR C 299 ARG 0.002 0.000 ARG C 165 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.600 Fit side-chains REVERT: A 94 GLN cc_start: 0.8145 (mp10) cc_final: 0.7856 (mp10) REVERT: A 359 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.8001 (t80) REVERT: A 383 MET cc_start: 0.6952 (mmp) cc_final: 0.6586 (mtp) REVERT: B 359 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.8061 (t80) REVERT: C 350 SER cc_start: 0.8365 (OUTLIER) cc_final: 0.8155 (m) REVERT: C 383 MET cc_start: 0.7111 (mmp) cc_final: 0.6672 (mtm) REVERT: D 359 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8217 (t80) REVERT: D 383 MET cc_start: 0.6946 (mmp) cc_final: 0.6689 (mtp) REVERT: D 391 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6589 (ttp-170) REVERT: E 94 GLN cc_start: 0.8155 (mp10) cc_final: 0.7813 (mp10) REVERT: E 350 SER cc_start: 0.8546 (t) cc_final: 0.8180 (p) REVERT: E 355 MET cc_start: 0.8390 (ttm) cc_final: 0.8170 (ttm) REVERT: E 383 MET cc_start: 0.7017 (mmp) cc_final: 0.6526 (mtp) outliers start: 26 outliers final: 10 residues processed: 161 average time/residue: 1.3581 time to fit residues: 238.0238 Evaluate side-chains 157 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN D 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13085 Z= 0.212 Angle : 0.460 5.274 17685 Z= 0.244 Chirality : 0.040 0.231 2050 Planarity : 0.004 0.039 2235 Dihedral : 3.904 14.286 1720 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.70 % Allowed : 9.26 % Favored : 89.05 % 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: 3.37 (0.21), residues: 1585 helix: 2.83 (0.15), residues: 1070 sheet: 2.00 (0.40), residues: 145 loop : 0.47 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 162 HIS 0.002 0.000 HIS C 122 PHE 0.019 0.002 PHE D 352 TYR 0.017 0.002 TYR B 299 ARG 0.004 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.662 Fit side-chains REVERT: A 94 GLN cc_start: 0.8123 (mp10) cc_final: 0.7851 (mp10) REVERT: A 359 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7853 (t80) REVERT: A 383 MET cc_start: 0.6902 (mmp) cc_final: 0.6541 (mtp) REVERT: B 390 ARG cc_start: 0.6729 (OUTLIER) cc_final: 0.6377 (mpt180) REVERT: C 350 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.8175 (m) REVERT: C 383 MET cc_start: 0.6989 (mmp) cc_final: 0.6529 (mtm) REVERT: D 383 MET cc_start: 0.6850 (mmp) cc_final: 0.6507 (mtp) REVERT: D 391 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6560 (ttp-170) REVERT: E 94 GLN cc_start: 0.8175 (mp10) cc_final: 0.7766 (mp10) REVERT: E 350 SER cc_start: 0.8544 (t) cc_final: 0.8175 (p) REVERT: E 355 MET cc_start: 0.8414 (ttm) cc_final: 0.8171 (ttm) REVERT: E 383 MET cc_start: 0.6996 (mmp) cc_final: 0.6514 (mtp) outliers start: 24 outliers final: 10 residues processed: 168 average time/residue: 1.3631 time to fit residues: 250.5584 Evaluate side-chains 166 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 359 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 ASN D 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 13085 Z= 0.232 Angle : 0.474 9.374 17685 Z= 0.249 Chirality : 0.040 0.229 2050 Planarity : 0.004 0.039 2235 Dihedral : 3.896 14.294 1720 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.48 % Allowed : 10.18 % Favored : 88.34 % 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: 3.35 (0.21), residues: 1585 helix: 2.82 (0.15), residues: 1070 sheet: 1.92 (0.40), residues: 145 loop : 0.53 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 375 HIS 0.002 0.000 HIS C 122 PHE 0.020 0.002 PHE D 352 TYR 0.020 0.002 TYR C 299 ARG 0.005 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 1.670 Fit side-chains REVERT: A 94 GLN cc_start: 0.8126 (mp10) cc_final: 0.7784 (mp10) REVERT: A 359 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.8043 (t80) REVERT: A 383 MET cc_start: 0.6876 (mmp) cc_final: 0.6520 (mtp) REVERT: B 359 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7781 (t80) REVERT: C 383 MET cc_start: 0.6942 (mmp) cc_final: 0.6506 (mtm) REVERT: D 318 ASP cc_start: 0.7889 (m-30) cc_final: 0.7686 (m-30) REVERT: D 359 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7869 (t80) REVERT: D 383 MET cc_start: 0.6854 (mmp) cc_final: 0.6507 (mtp) REVERT: D 391 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6586 (ttp-170) REVERT: E 94 GLN cc_start: 0.8168 (mp10) cc_final: 0.7741 (mp10) REVERT: E 355 MET cc_start: 0.8398 (ttm) cc_final: 0.8156 (ttm) REVERT: E 383 MET cc_start: 0.6970 (mmp) cc_final: 0.6492 (mtp) outliers start: 21 outliers final: 9 residues processed: 164 average time/residue: 1.2950 time to fit residues: 232.7508 Evaluate side-chains 163 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13085 Z= 0.269 Angle : 0.485 5.357 17685 Z= 0.256 Chirality : 0.041 0.237 2050 Planarity : 0.004 0.039 2235 Dihedral : 3.943 14.230 1720 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.48 % Allowed : 10.25 % Favored : 88.27 % 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: 3.29 (0.21), residues: 1585 helix: 2.77 (0.15), residues: 1070 sheet: 1.88 (0.40), residues: 145 loop : 0.51 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 375 HIS 0.002 0.000 HIS C 122 PHE 0.021 0.002 PHE D 352 TYR 0.024 0.002 TYR C 299 ARG 0.004 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.636 Fit side-chains REVERT: A 94 GLN cc_start: 0.8133 (mp10) cc_final: 0.7758 (mp10) REVERT: A 359 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7932 (t80) REVERT: A 383 MET cc_start: 0.6819 (mmp) cc_final: 0.6479 (mtp) REVERT: B 359 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7799 (t80) REVERT: C 383 MET cc_start: 0.7039 (mmp) cc_final: 0.6590 (mtm) REVERT: D 359 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7824 (t80) REVERT: D 383 MET cc_start: 0.6867 (mmp) cc_final: 0.6520 (mtp) REVERT: D 391 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6589 (ttp-170) REVERT: E 94 GLN cc_start: 0.8178 (mp10) cc_final: 0.7769 (mp10) REVERT: E 349 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8599 (mp) REVERT: E 355 MET cc_start: 0.8409 (ttm) cc_final: 0.8180 (ttm) REVERT: E 383 MET cc_start: 0.6948 (mmp) cc_final: 0.6473 (mtp) outliers start: 21 outliers final: 10 residues processed: 161 average time/residue: 1.2814 time to fit residues: 225.5838 Evaluate side-chains 165 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 ASN D 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13085 Z= 0.180 Angle : 0.456 10.181 17685 Z= 0.241 Chirality : 0.040 0.242 2050 Planarity : 0.003 0.040 2235 Dihedral : 3.800 14.671 1720 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.99 % Allowed : 10.95 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.45 (0.21), residues: 1585 helix: 2.89 (0.15), residues: 1070 sheet: 1.95 (0.40), residues: 145 loop : 0.58 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 162 HIS 0.002 0.000 HIS C 122 PHE 0.021 0.001 PHE E 352 TYR 0.021 0.002 TYR C 299 ARG 0.004 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.596 Fit side-chains REVERT: A 94 GLN cc_start: 0.8127 (mp10) cc_final: 0.7791 (mp10) REVERT: A 359 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7966 (t80) REVERT: A 383 MET cc_start: 0.6830 (mmp) cc_final: 0.6477 (mtp) REVERT: C 383 MET cc_start: 0.6886 (mmp) cc_final: 0.6462 (mtm) REVERT: D 359 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7629 (t80) REVERT: D 383 MET cc_start: 0.6800 (mmp) cc_final: 0.6461 (mtp) REVERT: E 94 GLN cc_start: 0.8163 (mp10) cc_final: 0.7768 (mp10) REVERT: E 349 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8566 (mp) REVERT: E 355 MET cc_start: 0.8360 (ttm) cc_final: 0.8152 (ttm) REVERT: E 383 MET cc_start: 0.6860 (mmp) cc_final: 0.6381 (mtp) outliers start: 14 outliers final: 5 residues processed: 167 average time/residue: 1.3324 time to fit residues: 243.7089 Evaluate side-chains 155 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN E 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13085 Z= 0.174 Angle : 0.454 8.187 17685 Z= 0.241 Chirality : 0.039 0.256 2050 Planarity : 0.003 0.040 2235 Dihedral : 3.763 14.773 1720 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.13 % Allowed : 10.95 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.51 (0.21), residues: 1585 helix: 2.93 (0.15), residues: 1070 sheet: 1.99 (0.40), residues: 145 loop : 0.63 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 162 HIS 0.002 0.000 HIS C 122 PHE 0.029 0.001 PHE E 395 TYR 0.016 0.001 TYR D 299 ARG 0.004 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 1.727 Fit side-chains REVERT: A 94 GLN cc_start: 0.8122 (mp10) cc_final: 0.7795 (mp10) REVERT: A 359 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7750 (t80) REVERT: A 383 MET cc_start: 0.6889 (mmp) cc_final: 0.6525 (mtp) REVERT: B 359 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7743 (t80) REVERT: C 383 MET cc_start: 0.6840 (mmp) cc_final: 0.6413 (mtm) REVERT: D 359 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7583 (t80) REVERT: D 383 MET cc_start: 0.6805 (mmp) cc_final: 0.6469 (mtp) REVERT: E 94 GLN cc_start: 0.8169 (mp10) cc_final: 0.7779 (mp10) REVERT: E 349 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8508 (mp) REVERT: E 355 MET cc_start: 0.8420 (ttm) cc_final: 0.8179 (ttm) REVERT: E 383 MET cc_start: 0.6865 (mmp) cc_final: 0.6369 (mtp) outliers start: 16 outliers final: 7 residues processed: 165 average time/residue: 1.3137 time to fit residues: 236.6663 Evaluate side-chains 161 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 102 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN E 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13085 Z= 0.193 Angle : 0.465 10.376 17685 Z= 0.245 Chirality : 0.040 0.247 2050 Planarity : 0.003 0.038 2235 Dihedral : 3.767 14.748 1720 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.92 % Allowed : 11.31 % Favored : 87.77 % 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: 3.50 (0.21), residues: 1585 helix: 2.91 (0.15), residues: 1070 sheet: 2.01 (0.40), residues: 145 loop : 0.63 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 162 HIS 0.002 0.000 HIS C 122 PHE 0.031 0.002 PHE E 395 TYR 0.018 0.001 TYR C 299 ARG 0.004 0.000 ARG A 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3170 Ramachandran restraints generated. 1585 Oldfield, 0 Emsley, 1585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 1.612 Fit side-chains REVERT: A 94 GLN cc_start: 0.8131 (mp10) cc_final: 0.7805 (mp10) REVERT: A 381 MET cc_start: 0.7542 (ttm) cc_final: 0.7208 (mtp) REVERT: A 383 MET cc_start: 0.7021 (mmp) cc_final: 0.6650 (mtp) REVERT: C 383 MET cc_start: 0.6804 (mmp) cc_final: 0.6334 (mtm) REVERT: D 359 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7580 (t80) REVERT: D 383 MET cc_start: 0.6814 (mmp) cc_final: 0.6470 (mtp) REVERT: E 94 GLN cc_start: 0.8184 (mp10) cc_final: 0.7796 (mp10) REVERT: E 349 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8481 (mp) REVERT: E 355 MET cc_start: 0.8340 (ttm) cc_final: 0.8097 (ttm) REVERT: E 383 MET cc_start: 0.6858 (mmp) cc_final: 0.6369 (mtp) outliers start: 13 outliers final: 6 residues processed: 156 average time/residue: 1.3214 time to fit residues: 225.5749 Evaluate side-chains 155 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 0.4980 chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN E 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.110791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.082368 restraints weight = 19525.388| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.51 r_work: 0.2937 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13085 Z= 0.202 Angle : 0.467 10.303 17685 Z= 0.246 Chirality : 0.039 0.253 2050 Planarity : 0.003 0.038 2235 Dihedral : 3.784 14.685 1720 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.85 % Allowed : 11.38 % Favored : 87.77 % 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: 3.50 (0.21), residues: 1585 helix: 2.91 (0.15), residues: 1070 sheet: 2.01 (0.40), residues: 145 loop : 0.64 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 162 HIS 0.002 0.000 HIS C 122 PHE 0.031 0.002 PHE E 395 TYR 0.022 0.002 TYR C 299 ARG 0.004 0.000 ARG C 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4132.60 seconds wall clock time: 76 minutes 10.96 seconds (4570.96 seconds total)