Starting phenix.real_space_refine on Fri Mar 15 21:43:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip3_35630/03_2024/8ip3_35630.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip3_35630/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip3_35630/03_2024/8ip3_35630.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip3_35630/03_2024/8ip3_35630.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip3_35630/03_2024/8ip3_35630.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip3_35630/03_2024/8ip3_35630.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'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} Time building chain proxies: 8.16, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.61 Conformation dependent library (CDL) restraints added in 2.5 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: 1.41 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: 4.05 Time building geometry restraints manager: 5.99 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: 99.13 - 106.10: 218 106.10 - 113.08: 7280 113.08 - 120.05: 4459 120.05 - 127.02: 5606 127.02 - 133.99: 122 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 2.440 nonbonded pdb=" OG SER E 99 " pdb=" OH TYR E 154 " model vdw 2.255 2.440 nonbonded pdb=" OG SER C 99 " pdb=" OH TYR C 154 " model vdw 2.255 2.440 nonbonded pdb=" OG SER B 99 " pdb=" OH TYR B 154 " model vdw 2.255 2.440 nonbonded pdb=" OG SER A 99 " pdb=" OH TYR A 154 " model vdw 2.256 2.440 ... (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 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.470 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 39.110 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:13.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.810 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.632 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: 1.3217 time to fit residues: 298.8940 Evaluate side-chains 152 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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: 0.0770 chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 40 optimal weight: 8.9990 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: 2.9990 chunk 90 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 362 ASN B 121 GLN B 362 ASN C 362 ASN D 121 GLN D 362 ASN E 121 GLN E 362 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1169 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= 0.337 Angle : 0.518 7.910 17685 Z= 0.267 Chirality : 0.042 0.215 2050 Planarity : 0.004 0.032 2235 Dihedral : 3.955 14.483 1720 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.27 % Allowed : 6.57 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.49 (0.21), residues: 1585 helix: 3.16 (0.15), residues: 1040 sheet: 2.10 (0.40), residues: 145 loop : -0.04 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 196 HIS 0.002 0.001 HIS E 122 PHE 0.023 0.002 PHE A 395 TYR 0.024 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 180 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 1.711 Fit side-chains REVERT: A 94 GLN cc_start: 0.8155 (mp10) cc_final: 0.7821 (mp10) REVERT: A 383 MET cc_start: 0.6941 (mmp) cc_final: 0.6569 (mtp) REVERT: C 350 SER cc_start: 0.8464 (t) cc_final: 0.8215 (m) REVERT: C 383 MET cc_start: 0.7005 (mmp) cc_final: 0.6546 (mtm) REVERT: D 350 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8572 (p) REVERT: D 383 MET cc_start: 0.6927 (mmp) cc_final: 0.6554 (mtp) REVERT: E 94 GLN cc_start: 0.8184 (mp10) cc_final: 0.7808 (mp10) REVERT: E 350 SER cc_start: 0.8583 (t) cc_final: 0.8200 (p) REVERT: E 355 MET cc_start: 0.8336 (ttm) cc_final: 0.8013 (ttm) REVERT: E 383 MET cc_start: 0.7020 (mmp) cc_final: 0.6487 (mtp) outliers start: 18 outliers final: 8 residues processed: 170 average time/residue: 1.1778 time to fit residues: 219.3914 Evaluate side-chains 157 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 SER 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 Chi-restraints excluded: chain D residue 385 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 152 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 E 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1196 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= 0.214 Angle : 0.459 8.929 17685 Z= 0.241 Chirality : 0.039 0.210 2050 Planarity : 0.003 0.035 2235 Dihedral : 3.849 15.060 1720 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.77 % Allowed : 7.28 % Favored : 90.95 % 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: 3.56 (0.21), residues: 1585 helix: 2.99 (0.15), residues: 1070 sheet: 2.14 (0.40), residues: 145 loop : 0.48 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 196 HIS 0.002 0.000 HIS C 122 PHE 0.019 0.002 PHE A 352 TYR 0.017 0.001 TYR C 299 ARG 0.003 0.000 ARG C 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 189 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.745 Fit side-chains REVERT: A 94 GLN cc_start: 0.8094 (mp10) cc_final: 0.7754 (mp10) REVERT: A 359 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.8021 (t80) REVERT: A 383 MET cc_start: 0.6854 (mmp) cc_final: 0.6502 (mtp) REVERT: B 344 MET cc_start: 0.8723 (mtm) cc_final: 0.8496 (mtp) REVERT: B 355 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8160 (ttp) REVERT: B 383 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6362 (mpp) REVERT: C 383 MET cc_start: 0.6934 (mmp) cc_final: 0.6502 (mtm) REVERT: D 359 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7845 (t80) REVERT: D 383 MET cc_start: 0.6907 (mmp) cc_final: 0.6515 (mtp) REVERT: E 94 GLN cc_start: 0.8212 (mp10) cc_final: 0.7852 (mp10) REVERT: E 350 SER cc_start: 0.8593 (t) cc_final: 0.8256 (p) REVERT: E 355 MET cc_start: 0.8365 (ttm) cc_final: 0.8049 (ttm) REVERT: E 383 MET cc_start: 0.7016 (mmp) cc_final: 0.6482 (mtp) outliers start: 25 outliers final: 11 residues processed: 172 average time/residue: 1.1830 time to fit residues: 223.0859 Evaluate side-chains 173 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 385 SER 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 383 MET Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain D residue 96 ASN 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 385 SER 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: 3.9990 chunk 106 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 141 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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: 0.8214 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13085 Z= 0.252 Angle : 0.476 8.957 17685 Z= 0.248 Chirality : 0.040 0.211 2050 Planarity : 0.003 0.036 2235 Dihedral : 3.879 15.181 1720 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.98 % Allowed : 8.20 % Favored : 89.82 % 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: 3.53 (0.21), residues: 1585 helix: 2.95 (0.15), residues: 1070 sheet: 2.13 (0.40), residues: 145 loop : 0.53 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 375 HIS 0.002 0.000 HIS C 122 PHE 0.020 0.002 PHE D 395 TYR 0.021 0.002 TYR C 299 ARG 0.005 0.000 ARG C 372 *********************** 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 191 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 163 time to evaluate : 1.555 Fit side-chains REVERT: A 94 GLN cc_start: 0.8117 (mp10) cc_final: 0.7779 (mp10) REVERT: A 359 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7916 (t80) REVERT: A 383 MET cc_start: 0.6911 (mmp) cc_final: 0.6546 (mtp) REVERT: B 359 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7899 (t80) REVERT: B 383 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6389 (mpp) REVERT: C 383 MET cc_start: 0.6948 (mmp) cc_final: 0.6518 (mtm) REVERT: D 359 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.8048 (t80) REVERT: D 383 MET cc_start: 0.6856 (mmp) cc_final: 0.6504 (mtp) REVERT: D 391 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6505 (ttp-170) REVERT: E 94 GLN cc_start: 0.8186 (mp10) cc_final: 0.7810 (mp10) REVERT: E 350 SER cc_start: 0.8568 (t) cc_final: 0.8201 (p) REVERT: E 355 MET cc_start: 0.8366 (ttm) cc_final: 0.8077 (ttm) REVERT: E 383 MET cc_start: 0.6976 (mmp) cc_final: 0.6438 (mtp) outliers start: 28 outliers final: 12 residues processed: 176 average time/residue: 1.1783 time to fit residues: 227.1467 Evaluate side-chains 176 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 257 GLU 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 C residue 197 ILE Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain D residue 96 ASN 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 385 SER Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 0.2980 chunk 134 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- 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: 0.8214 moved from start: 0.1441 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= 0.249 Angle : 0.469 5.361 17685 Z= 0.248 Chirality : 0.040 0.222 2050 Planarity : 0.003 0.036 2235 Dihedral : 3.883 15.424 1720 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.05 % Allowed : 8.34 % Favored : 89.61 % 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: 3.52 (0.21), residues: 1585 helix: 3.16 (0.15), residues: 1040 sheet: 2.13 (0.40), residues: 145 loop : 0.05 (0.36), residues: 400 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 C 352 TYR 0.022 0.002 TYR C 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 191 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 1.813 Fit side-chains REVERT: A 94 GLN cc_start: 0.8115 (mp10) cc_final: 0.7776 (mp10) REVERT: A 359 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7950 (t80) REVERT: A 383 MET cc_start: 0.6926 (mmp) cc_final: 0.6562 (mtp) REVERT: B 355 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8200 (ttp) REVERT: B 359 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7832 (t80) REVERT: B 383 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6396 (mpp) REVERT: C 383 MET cc_start: 0.6936 (mmp) cc_final: 0.6492 (mtm) REVERT: D 359 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8072 (t80) REVERT: D 383 MET cc_start: 0.6846 (mmp) cc_final: 0.6497 (mtp) REVERT: D 391 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6473 (ttp-170) REVERT: E 94 GLN cc_start: 0.8181 (mp10) cc_final: 0.7802 (mp10) REVERT: E 350 SER cc_start: 0.8548 (t) cc_final: 0.8178 (p) REVERT: E 355 MET cc_start: 0.8384 (ttm) cc_final: 0.8121 (ttm) REVERT: E 383 MET cc_start: 0.6971 (mmp) cc_final: 0.6435 (mtp) outliers start: 29 outliers final: 15 residues processed: 175 average time/residue: 1.2489 time to fit residues: 238.9855 Evaluate side-chains 178 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 157 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 257 GLU 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 C residue 197 ILE Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 257 GLU 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 385 SER 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 385 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 149 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 E 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1437 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= 0.213 Angle : 0.463 9.640 17685 Z= 0.242 Chirality : 0.040 0.257 2050 Planarity : 0.003 0.036 2235 Dihedral : 3.835 15.563 1720 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.98 % Allowed : 9.12 % Favored : 88.90 % 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: 3.54 (0.21), residues: 1585 helix: 2.95 (0.15), residues: 1070 sheet: 2.11 (0.40), residues: 145 loop : 0.55 (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 0.001 PHE C 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 195 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 1.716 Fit side-chains REVERT: A 94 GLN cc_start: 0.8116 (mp10) cc_final: 0.7779 (mp10) REVERT: A 359 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.8010 (t80) REVERT: A 383 MET cc_start: 0.6891 (mmp) cc_final: 0.6527 (mtp) REVERT: B 359 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7722 (t80) REVERT: B 383 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6383 (mpp) REVERT: C 383 MET cc_start: 0.6923 (mmp) cc_final: 0.6482 (mtm) REVERT: D 359 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.8062 (t80) REVERT: D 383 MET cc_start: 0.6821 (mmp) cc_final: 0.6474 (mtp) REVERT: D 391 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6466 (ttp-170) REVERT: E 94 GLN cc_start: 0.8179 (mp10) cc_final: 0.7797 (mp10) REVERT: E 350 SER cc_start: 0.8557 (t) cc_final: 0.8174 (p) REVERT: E 355 MET cc_start: 0.8289 (ttm) cc_final: 0.8024 (ttm) REVERT: E 383 MET cc_start: 0.6901 (mmp) cc_final: 0.6371 (mtp) outliers start: 28 outliers final: 17 residues processed: 178 average time/residue: 1.1703 time to fit residues: 228.6341 Evaluate side-chains 179 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 157 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 257 GLU 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 C residue 197 ILE Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 257 GLU 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 385 SER 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 Chi-restraints excluded: chain E residue 385 SER 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: 0.6980 chunk 109 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 ASN C 362 ASN D 121 GLN E 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13085 Z= 0.280 Angle : 0.487 5.384 17685 Z= 0.255 Chirality : 0.041 0.238 2050 Planarity : 0.004 0.036 2235 Dihedral : 3.922 15.387 1720 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.91 % Allowed : 9.40 % Favored : 88.69 % 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: 3.10 (0.15), residues: 1040 sheet: 2.10 (0.40), residues: 145 loop : 0.05 (0.36), residues: 400 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 0.020 0.002 PHE D 352 TYR 0.025 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 190 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 163 time to evaluate : 1.460 Fit side-chains REVERT: A 94 GLN cc_start: 0.8127 (mp10) cc_final: 0.7786 (mp10) REVERT: A 359 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.8026 (t80) REVERT: A 383 MET cc_start: 0.6940 (mmp) cc_final: 0.6581 (mtp) REVERT: B 359 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7811 (t80) REVERT: B 383 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6446 (mpp) REVERT: C 383 MET cc_start: 0.6995 (mmp) cc_final: 0.6562 (mtm) REVERT: D 383 MET cc_start: 0.6862 (mmp) cc_final: 0.6517 (mtp) REVERT: D 391 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6463 (ttp-170) REVERT: E 94 GLN cc_start: 0.8175 (mp10) cc_final: 0.7790 (mp10) REVERT: E 355 MET cc_start: 0.8414 (ttm) cc_final: 0.8176 (ttm) REVERT: E 383 MET cc_start: 0.6967 (mmp) cc_final: 0.6440 (mtp) outliers start: 27 outliers final: 17 residues processed: 174 average time/residue: 1.2108 time to fit residues: 230.3625 Evaluate side-chains 171 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 257 GLU 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 385 SER 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 Chi-restraints excluded: chain E residue 385 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 ASN E 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13085 Z= 0.200 Angle : 0.462 10.148 17685 Z= 0.242 Chirality : 0.040 0.270 2050 Planarity : 0.003 0.038 2235 Dihedral : 3.822 15.769 1720 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.63 % Allowed : 10.18 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.21), residues: 1585 helix: 2.95 (0.15), residues: 1070 sheet: 2.11 (0.40), residues: 145 loop : 0.55 (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 0.020 0.001 PHE E 352 TYR 0.021 0.002 TYR C 299 ARG 0.004 0.000 ARG C 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 190 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 167 time to evaluate : 1.637 Fit side-chains REVERT: A 94 GLN cc_start: 0.8109 (mp10) cc_final: 0.7769 (mp10) REVERT: A 359 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.8017 (t80) REVERT: A 383 MET cc_start: 0.6840 (mmp) cc_final: 0.6471 (mtp) REVERT: B 383 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6398 (mpp) REVERT: C 383 MET cc_start: 0.6922 (mmp) cc_final: 0.6480 (mtm) REVERT: D 359 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7813 (t80) REVERT: D 383 MET cc_start: 0.6806 (mmp) cc_final: 0.6459 (mtp) REVERT: D 391 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6486 (ttp-170) REVERT: E 94 GLN cc_start: 0.8177 (mp10) cc_final: 0.7798 (mp10) REVERT: E 349 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8557 (mp) REVERT: E 355 MET cc_start: 0.8366 (ttm) cc_final: 0.8132 (ttm) REVERT: E 383 MET cc_start: 0.6903 (mmp) cc_final: 0.6369 (mtp) outliers start: 23 outliers final: 12 residues processed: 177 average time/residue: 1.2093 time to fit residues: 234.8426 Evaluate side-chains 175 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 1.548 ------------------------------------------------------------------------------- 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 383 MET Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain D residue 96 ASN 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 385 SER Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 385 SER 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: 0.7980 chunk 139 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN E 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1538 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= 0.224 Angle : 0.472 8.250 17685 Z= 0.247 Chirality : 0.040 0.254 2050 Planarity : 0.003 0.039 2235 Dihedral : 3.836 15.698 1720 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.27 % Allowed : 10.74 % Favored : 87.99 % 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: 2.06 (0.40), residues: 145 loop : 0.56 (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 E 352 TYR 0.024 0.002 TYR C 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 fitting. rotamer outliers: 18 poor density : 158 time to evaluate : 1.665 Fit side-chains REVERT: A 94 GLN cc_start: 0.8117 (mp10) cc_final: 0.7778 (mp10) REVERT: A 359 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.8134 (t80) REVERT: A 383 MET cc_start: 0.6823 (mmp) cc_final: 0.6488 (mtp) REVERT: B 359 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7671 (t80) REVERT: B 383 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6411 (mpp) REVERT: C 383 MET cc_start: 0.6982 (mmp) cc_final: 0.6519 (mtm) REVERT: D 383 MET cc_start: 0.6829 (mmp) cc_final: 0.6482 (mtp) REVERT: D 391 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6484 (ttp-170) REVERT: E 94 GLN cc_start: 0.8182 (mp10) cc_final: 0.7803 (mp10) REVERT: E 349 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8552 (mp) REVERT: E 355 MET cc_start: 0.8327 (ttm) cc_final: 0.8090 (ttm) REVERT: E 383 MET cc_start: 0.6907 (mmp) cc_final: 0.6373 (mtp) outliers start: 18 outliers final: 12 residues processed: 165 average time/residue: 1.1627 time to fit residues: 210.5969 Evaluate side-chains 171 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE 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 359 PHE Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 385 SER Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 385 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 102 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13085 Z= 0.196 Angle : 0.467 10.452 17685 Z= 0.243 Chirality : 0.040 0.260 2050 Planarity : 0.003 0.039 2235 Dihedral : 3.795 15.845 1720 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.41 % Allowed : 10.53 % 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: 3.55 (0.21), residues: 1585 helix: 2.97 (0.15), residues: 1070 sheet: 2.05 (0.40), residues: 145 loop : 0.56 (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 0.020 0.001 PHE C 352 TYR 0.023 0.002 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 182 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 1.568 Fit side-chains REVERT: A 94 GLN cc_start: 0.8115 (mp10) cc_final: 0.7779 (mp10) REVERT: A 383 MET cc_start: 0.6782 (mmp) cc_final: 0.6434 (mtp) REVERT: B 359 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7650 (t80) REVERT: C 383 MET cc_start: 0.6858 (mmp) cc_final: 0.6396 (mtm) REVERT: D 359 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7614 (t80) REVERT: D 383 MET cc_start: 0.6827 (mmp) cc_final: 0.6464 (mtp) REVERT: D 391 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6470 (ttp-170) REVERT: E 94 GLN cc_start: 0.8173 (mp10) cc_final: 0.7792 (mp10) REVERT: E 349 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8530 (mp) REVERT: E 355 MET cc_start: 0.8315 (ttm) cc_final: 0.8059 (ttm) REVERT: E 383 MET cc_start: 0.6872 (mmp) cc_final: 0.6348 (mtp) outliers start: 20 outliers final: 11 residues processed: 168 average time/residue: 1.1613 time to fit residues: 214.7570 Evaluate side-chains 170 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 155 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE 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 336 MET Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain D residue 96 ASN 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 D residue 385 SER Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 385 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 34 optimal weight: 0.0870 chunk 123 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN E 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.083408 restraints weight = 19525.180| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.50 r_work: 0.2951 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1476 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= 0.180 Angle : 0.460 10.480 17685 Z= 0.241 Chirality : 0.039 0.257 2050 Planarity : 0.003 0.039 2235 Dihedral : 3.756 15.956 1720 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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 (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: 3.60 (0.21), residues: 1585 helix: 3.01 (0.15), residues: 1070 sheet: 2.00 (0.40), residues: 145 loop : 0.58 (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 0.029 0.001 PHE E 395 TYR 0.023 0.002 TYR C 299 ARG 0.004 0.000 ARG A 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4225.53 seconds wall clock time: 75 minutes 55.55 seconds (4555.55 seconds total)