Starting phenix.real_space_refine on Wed Feb 4 19:36:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ip3_35630/02_2026/8ip3_35630.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ip3_35630/02_2026/8ip3_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_35630/02_2026/8ip3_35630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ip3_35630/02_2026/8ip3_35630.map" model { file = "/net/cci-nas-00/data/ceres_data/8ip3_35630/02_2026/8ip3_35630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ip3_35630/02_2026/8ip3_35630.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12868 Number of models: 1 Model: "" Number of chains: 10 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: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" 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: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" 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: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" 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: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" 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: {'GLU:plan': 3, 'GLN:plan1': 2, '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} Time building chain proxies: 2.61, per 1000 atoms: 0.20 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: 0.76 Conformation dependent library (CDL) restraints added in 470.0 milliseconds 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: 0.25 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: 1.85 Time building geometry restraints manager: 0.98 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: 1.120 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.400 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.960 ------------------------------------------------------------------------------- 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= 0.116 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG B 136 TYR 0.012 0.001 TYR E 299 PHE 0.016 0.001 PHE D 352 TRP 0.008 0.001 TRP A 162 HIS 0.001 0.000 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00236 (13085) covalent geometry : angle 0.42491 (17685) hydrogen bonds : bond 0.08434 ( 1015) hydrogen bonds : angle 4.40704 ( 2970) *********************** 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 : 0.520 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: 0.5754 time to fit residues: 129.6720 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 : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.079541 restraints weight = 19813.057| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.54 r_work: 0.2880 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1346 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= 0.259 Angle : 0.556 7.963 17685 Z= 0.288 Chirality : 0.043 0.227 2050 Planarity : 0.004 0.033 2235 Dihedral : 4.089 14.350 1720 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.06 % Allowed : 6.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.40 (0.21), residues: 1585 helix: 3.09 (0.15), residues: 1020 sheet: 2.02 (0.39), residues: 145 loop : 0.15 (0.35), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 165 TYR 0.026 0.002 TYR C 299 PHE 0.023 0.002 PHE A 395 TRP 0.009 0.001 TRP E 196 HIS 0.003 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00605 (13085) covalent geometry : angle 0.55630 (17685) hydrogen bonds : bond 0.05398 ( 1015) hydrogen bonds : angle 4.17690 ( 2970) *********************** 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 166 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.399 Fit side-chains REVERT: A 94 GLN cc_start: 0.8220 (mp10) cc_final: 0.7815 (mp10) REVERT: A 383 MET cc_start: 0.6983 (mmp) cc_final: 0.6322 (mtp) REVERT: C 350 SER cc_start: 0.8003 (t) cc_final: 0.7776 (m) REVERT: C 383 MET cc_start: 0.6948 (mmp) cc_final: 0.6265 (mtm) REVERT: D 350 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8097 (p) REVERT: D 383 MET cc_start: 0.6884 (mmp) cc_final: 0.6225 (mtp) REVERT: E 94 GLN cc_start: 0.8256 (mp10) cc_final: 0.7733 (mp10) REVERT: E 350 SER cc_start: 0.8154 (t) cc_final: 0.7940 (m) REVERT: E 355 MET cc_start: 0.7990 (ttm) cc_final: 0.7737 (ttm) REVERT: E 383 MET cc_start: 0.6984 (mmp) cc_final: 0.6193 (mtp) outliers start: 15 outliers final: 6 residues processed: 156 average time/residue: 0.5755 time to fit residues: 97.3218 Evaluate side-chains 142 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 314 ARG 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 128 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN D 121 GLN E 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.109637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.080847 restraints weight = 19944.318| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.54 r_work: 0.2908 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13085 Z= 0.179 Angle : 0.484 5.336 17685 Z= 0.256 Chirality : 0.040 0.213 2050 Planarity : 0.004 0.036 2235 Dihedral : 3.977 14.342 1720 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.77 % Allowed : 7.21 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.42 (0.21), residues: 1585 helix: 2.86 (0.15), residues: 1050 sheet: 2.03 (0.40), residues: 145 loop : 0.68 (0.36), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 165 TYR 0.019 0.002 TYR C 299 PHE 0.020 0.002 PHE A 352 TRP 0.008 0.001 TRP B 375 HIS 0.002 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00408 (13085) covalent geometry : angle 0.48351 (17685) hydrogen bonds : bond 0.04998 ( 1015) hydrogen bonds : angle 4.03670 ( 2970) *********************** 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 179 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.367 Fit side-chains REVERT: A 94 GLN cc_start: 0.8177 (mp10) cc_final: 0.7767 (mp10) REVERT: A 359 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7659 (t80) REVERT: A 383 MET cc_start: 0.6812 (mmp) cc_final: 0.6200 (mtp) REVERT: B 355 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7778 (ttp) REVERT: B 359 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7810 (t80) REVERT: C 383 MET cc_start: 0.6921 (mmp) cc_final: 0.6198 (mtm) REVERT: D 359 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7694 (t80) REVERT: D 383 MET cc_start: 0.6869 (mmp) cc_final: 0.6239 (mtp) REVERT: D 391 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6560 (ttp-170) REVERT: E 94 GLN cc_start: 0.8212 (mp10) cc_final: 0.7778 (mp10) REVERT: E 355 MET cc_start: 0.8004 (ttm) cc_final: 0.7774 (ttm) REVERT: E 383 MET cc_start: 0.6951 (mmp) cc_final: 0.6166 (mtp) outliers start: 25 outliers final: 7 residues processed: 162 average time/residue: 0.5545 time to fit residues: 97.3671 Evaluate side-chains 160 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 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 D residue 391 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 20 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.108075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.079402 restraints weight = 19945.785| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.54 r_work: 0.2879 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1651 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= 0.247 Angle : 0.536 8.773 17685 Z= 0.279 Chirality : 0.042 0.242 2050 Planarity : 0.004 0.039 2235 Dihedral : 4.112 14.636 1720 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.48 % Allowed : 8.76 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.21), residues: 1585 helix: 2.85 (0.15), residues: 1040 sheet: 1.96 (0.40), residues: 145 loop : -0.03 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 165 TYR 0.026 0.002 TYR C 299 PHE 0.021 0.002 PHE A 352 TRP 0.009 0.001 TRP B 375 HIS 0.002 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00578 (13085) covalent geometry : angle 0.53563 (17685) hydrogen bonds : bond 0.05342 ( 1015) hydrogen bonds : angle 4.11728 ( 2970) *********************** 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 170 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.562 Fit side-chains REVERT: A 94 GLN cc_start: 0.8197 (mp10) cc_final: 0.7787 (mp10) REVERT: A 359 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7847 (t80) REVERT: A 383 MET cc_start: 0.7006 (mmp) cc_final: 0.6352 (mtp) REVERT: B 359 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7739 (t80) REVERT: B 390 ARG cc_start: 0.6292 (OUTLIER) cc_final: 0.6004 (mpt180) REVERT: C 383 MET cc_start: 0.7036 (mmp) cc_final: 0.6335 (mtm) REVERT: D 359 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7944 (t80) REVERT: D 383 MET cc_start: 0.6901 (mmp) cc_final: 0.6278 (mtp) REVERT: D 391 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6555 (ttp-170) REVERT: E 94 GLN cc_start: 0.8194 (mp10) cc_final: 0.7747 (mp10) REVERT: E 383 MET cc_start: 0.6959 (mmp) cc_final: 0.6178 (mtp) outliers start: 21 outliers final: 9 residues processed: 158 average time/residue: 0.5920 time to fit residues: 101.3797 Evaluate side-chains 155 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 B residue 390 ARG 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 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 359 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 23 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.110860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.082432 restraints weight = 19781.883| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.52 r_work: 0.2932 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13085 Z= 0.129 Angle : 0.450 5.264 17685 Z= 0.239 Chirality : 0.039 0.228 2050 Planarity : 0.003 0.039 2235 Dihedral : 3.850 14.439 1720 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.34 % Allowed : 9.47 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.21), residues: 1585 helix: 2.84 (0.15), residues: 1070 sheet: 1.98 (0.40), residues: 145 loop : 0.51 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 314 TYR 0.015 0.001 TYR E 299 PHE 0.020 0.001 PHE D 352 TRP 0.009 0.001 TRP B 162 HIS 0.002 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00274 (13085) covalent geometry : angle 0.44961 (17685) hydrogen bonds : bond 0.04699 ( 1015) hydrogen bonds : angle 3.93386 ( 2970) *********************** 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 183 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.532 Fit side-chains REVERT: A 94 GLN cc_start: 0.8177 (mp10) cc_final: 0.7716 (mp10) REVERT: A 147 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7975 (mm-30) REVERT: A 359 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7758 (t80) REVERT: A 383 MET cc_start: 0.6778 (mmp) cc_final: 0.6160 (mtp) REVERT: B 344 MET cc_start: 0.8703 (mtm) cc_final: 0.8493 (mtp) REVERT: B 362 ASN cc_start: 0.7951 (m110) cc_final: 0.7667 (m-40) REVERT: C 383 MET cc_start: 0.6913 (mmp) cc_final: 0.6182 (mtm) REVERT: D 383 MET cc_start: 0.6799 (mmp) cc_final: 0.6184 (mtp) REVERT: D 391 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6593 (ttp-170) REVERT: E 94 GLN cc_start: 0.8206 (mp10) cc_final: 0.7699 (mp10) REVERT: E 383 MET cc_start: 0.6838 (mmp) cc_final: 0.6063 (mtp) outliers start: 19 outliers final: 6 residues processed: 170 average time/residue: 0.5362 time to fit residues: 99.5804 Evaluate side-chains 162 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 355 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 391 ARG Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 1.9990 chunk 94 optimal weight: 0.3980 chunk 66 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.110878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.082586 restraints weight = 19599.207| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.50 r_work: 0.2936 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13085 Z= 0.134 Angle : 0.455 9.653 17685 Z= 0.241 Chirality : 0.039 0.228 2050 Planarity : 0.003 0.039 2235 Dihedral : 3.812 14.394 1720 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.34 % Allowed : 10.11 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.44 (0.21), residues: 1585 helix: 2.88 (0.15), residues: 1070 sheet: 1.97 (0.40), residues: 145 loop : 0.56 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 372 TYR 0.018 0.001 TYR C 299 PHE 0.021 0.001 PHE E 352 TRP 0.009 0.001 TRP E 162 HIS 0.002 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00291 (13085) covalent geometry : angle 0.45529 (17685) hydrogen bonds : bond 0.04712 ( 1015) hydrogen bonds : angle 3.89706 ( 2970) *********************** 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 182 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.499 Fit side-chains REVERT: A 94 GLN cc_start: 0.8202 (mp10) cc_final: 0.7742 (mp10) REVERT: A 147 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7940 (mm-30) REVERT: A 383 MET cc_start: 0.6732 (mmp) cc_final: 0.6117 (mtp) REVERT: C 383 MET cc_start: 0.6840 (mmp) cc_final: 0.6135 (mtm) REVERT: D 359 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7495 (t80) REVERT: D 383 MET cc_start: 0.6782 (mmp) cc_final: 0.6148 (mtp) REVERT: E 94 GLN cc_start: 0.8206 (mp10) cc_final: 0.7693 (mp10) REVERT: E 383 MET cc_start: 0.6786 (mmp) cc_final: 0.6012 (mtp) outliers start: 19 outliers final: 8 residues processed: 170 average time/residue: 0.5892 time to fit residues: 108.4689 Evaluate side-chains 162 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 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 E residue 338 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.111314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.083050 restraints weight = 19610.300| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.51 r_work: 0.2945 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13085 Z= 0.127 Angle : 0.447 8.231 17685 Z= 0.238 Chirality : 0.039 0.219 2050 Planarity : 0.003 0.039 2235 Dihedral : 3.765 14.451 1720 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.34 % Allowed : 10.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.21), residues: 1585 helix: 2.92 (0.15), residues: 1070 sheet: 1.99 (0.40), residues: 145 loop : 0.57 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.019 0.001 TYR C 299 PHE 0.021 0.001 PHE D 352 TRP 0.009 0.001 TRP E 162 HIS 0.002 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00269 (13085) covalent geometry : angle 0.44738 (17685) hydrogen bonds : bond 0.04646 ( 1015) hydrogen bonds : angle 3.85962 ( 2970) *********************** 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 177 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.480 Fit side-chains REVERT: A 94 GLN cc_start: 0.8188 (mp10) cc_final: 0.7730 (mp10) REVERT: A 147 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7943 (mm-30) REVERT: A 383 MET cc_start: 0.6849 (mmp) cc_final: 0.6190 (mtp) REVERT: B 359 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7409 (t80) REVERT: C 383 MET cc_start: 0.6745 (mmp) cc_final: 0.6054 (mtm) REVERT: D 359 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7356 (t80) REVERT: D 383 MET cc_start: 0.6771 (mmp) cc_final: 0.6138 (mtp) REVERT: E 94 GLN cc_start: 0.8209 (mp10) cc_final: 0.7700 (mp10) REVERT: E 383 MET cc_start: 0.6870 (mmp) cc_final: 0.6114 (mtp) outliers start: 19 outliers final: 9 residues processed: 165 average time/residue: 0.5750 time to fit residues: 103.0269 Evaluate side-chains 162 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE 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 355 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 E residue 338 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 114 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN D 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.109784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.081192 restraints weight = 19579.551| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.52 r_work: 0.2900 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13085 Z= 0.173 Angle : 0.489 10.064 17685 Z= 0.256 Chirality : 0.040 0.242 2050 Planarity : 0.004 0.037 2235 Dihedral : 3.871 14.305 1720 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.13 % Allowed : 11.02 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.39 (0.21), residues: 1585 helix: 2.83 (0.15), residues: 1070 sheet: 1.97 (0.40), residues: 145 loop : 0.57 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.018 0.002 TYR D 299 PHE 0.021 0.002 PHE D 352 TRP 0.008 0.001 TRP B 375 HIS 0.002 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00393 (13085) covalent geometry : angle 0.48887 (17685) hydrogen bonds : bond 0.04926 ( 1015) hydrogen bonds : angle 3.95861 ( 2970) *********************** 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 170 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.422 Fit side-chains REVERT: A 94 GLN cc_start: 0.8202 (mp10) cc_final: 0.7735 (mp10) REVERT: A 383 MET cc_start: 0.6775 (mmp) cc_final: 0.6147 (mtp) REVERT: B 359 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7469 (t80) REVERT: C 383 MET cc_start: 0.6872 (mmp) cc_final: 0.6171 (mtm) REVERT: D 359 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7400 (t80) REVERT: D 383 MET cc_start: 0.6785 (mmp) cc_final: 0.6155 (mtp) REVERT: E 94 GLN cc_start: 0.8235 (mp10) cc_final: 0.7791 (mp10) REVERT: E 383 MET cc_start: 0.6846 (mmp) cc_final: 0.6120 (mtp) outliers start: 16 outliers final: 11 residues processed: 159 average time/residue: 0.5649 time to fit residues: 97.3826 Evaluate side-chains 158 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 355 MET 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 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 154 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 126 optimal weight: 0.4980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN D 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.111184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.082764 restraints weight = 19828.394| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.53 r_work: 0.2948 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1527 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= 0.130 Angle : 0.459 10.509 17685 Z= 0.242 Chirality : 0.039 0.253 2050 Planarity : 0.003 0.038 2235 Dihedral : 3.767 14.701 1720 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.13 % Allowed : 11.17 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.48 (0.21), residues: 1585 helix: 2.91 (0.15), residues: 1070 sheet: 1.98 (0.40), residues: 145 loop : 0.59 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.017 0.001 TYR C 299 PHE 0.020 0.001 PHE E 352 TRP 0.009 0.001 TRP E 162 HIS 0.002 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00278 (13085) covalent geometry : angle 0.45940 (17685) hydrogen bonds : bond 0.04666 ( 1015) hydrogen bonds : angle 3.87585 ( 2970) *********************** 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 171 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.446 Fit side-chains REVERT: A 94 GLN cc_start: 0.8192 (mp10) cc_final: 0.7734 (mp10) REVERT: A 383 MET cc_start: 0.6937 (mmp) cc_final: 0.6271 (mtp) REVERT: B 359 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7454 (t80) REVERT: C 383 MET cc_start: 0.6745 (mmp) cc_final: 0.6041 (mtm) REVERT: D 359 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7281 (t80) REVERT: D 383 MET cc_start: 0.6766 (mmp) cc_final: 0.6133 (mtp) REVERT: E 94 GLN cc_start: 0.8209 (mp10) cc_final: 0.7700 (mp10) REVERT: E 350 SER cc_start: 0.7938 (m) cc_final: 0.7557 (p) REVERT: E 383 MET cc_start: 0.6850 (mmp) cc_final: 0.6093 (mtp) outliers start: 16 outliers final: 7 residues processed: 161 average time/residue: 0.5475 time to fit residues: 96.0106 Evaluate side-chains 160 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 314 ARG 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 1 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 98 optimal weight: 0.0370 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.8662 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.107526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.079328 restraints weight = 19772.134| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.45 r_work: 0.2897 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1531 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= 0.130 Angle : 0.460 10.319 17685 Z= 0.242 Chirality : 0.039 0.240 2050 Planarity : 0.003 0.038 2235 Dihedral : 3.740 14.740 1720 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.78 % Allowed : 11.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.52 (0.21), residues: 1585 helix: 2.94 (0.15), residues: 1070 sheet: 1.97 (0.40), residues: 145 loop : 0.61 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 372 TYR 0.019 0.001 TYR C 299 PHE 0.020 0.001 PHE D 352 TRP 0.009 0.001 TRP E 162 HIS 0.002 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00278 (13085) covalent geometry : angle 0.45952 (17685) hydrogen bonds : bond 0.04648 ( 1015) hydrogen bonds : angle 3.85762 ( 2970) ********************** 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 166 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.513 Fit side-chains REVERT: A 94 GLN cc_start: 0.8225 (mp10) cc_final: 0.7765 (mp10) REVERT: A 383 MET cc_start: 0.6981 (mmp) cc_final: 0.6289 (mtp) REVERT: C 383 MET cc_start: 0.6745 (mmp) cc_final: 0.5989 (mtm) REVERT: D 359 PHE cc_start: 0.7928 (OUTLIER) cc_final: 0.7256 (t80) REVERT: D 383 MET cc_start: 0.6786 (mmp) cc_final: 0.6120 (mtp) REVERT: E 94 GLN cc_start: 0.8258 (mp10) cc_final: 0.7760 (mp10) REVERT: E 350 SER cc_start: 0.8046 (m) cc_final: 0.7672 (p) REVERT: E 383 MET cc_start: 0.6866 (mmp) cc_final: 0.6063 (mtp) outliers start: 11 outliers final: 6 residues processed: 159 average time/residue: 0.5208 time to fit residues: 90.5416 Evaluate side-chains 154 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 122 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 ASN D 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.083130 restraints weight = 19585.476| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.52 r_work: 0.2951 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1526 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= 0.127 Angle : 0.458 10.514 17685 Z= 0.241 Chirality : 0.039 0.239 2050 Planarity : 0.003 0.038 2235 Dihedral : 3.720 14.788 1720 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.85 % Allowed : 11.31 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.54 (0.21), residues: 1585 helix: 2.96 (0.15), residues: 1070 sheet: 1.97 (0.40), residues: 145 loop : 0.62 (0.38), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 372 TYR 0.016 0.001 TYR D 299 PHE 0.020 0.001 PHE D 352 TRP 0.010 0.001 TRP E 162 HIS 0.002 0.000 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00270 (13085) covalent geometry : angle 0.45779 (17685) hydrogen bonds : bond 0.04619 ( 1015) hydrogen bonds : angle 3.83983 ( 2970) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3455.03 seconds wall clock time: 59 minutes 36.15 seconds (3576.15 seconds total)