Starting phenix.real_space_refine on Tue Dec 31 19:05:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d1l_27134/12_2024/8d1l_27134.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1l_27134/12_2024/8d1l_27134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d1l_27134/12_2024/8d1l_27134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1l_27134/12_2024/8d1l_27134.map" model { file = "/net/cci-nas-00/data/ceres_data/8d1l_27134/12_2024/8d1l_27134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1l_27134/12_2024/8d1l_27134.cif" } resolution = 2.12 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= -0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 P 5 5.49 5 S 80 5.16 5 Cl 1 4.86 5 C 10905 2.51 5 N 2550 2.21 5 O 2760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16306 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "A" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "B" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {' CA': 1, 'MC3': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 144 Unusual residues: {' CA': 1, ' CL': 1, 'MC3': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 41 Restraints were copied for chains: E, C, D Time building chain proxies: 11.61, per 1000 atoms: 0.71 Number of scatterers: 16306 At special positions: 0 Unit cell: (109.56, 107.07, 110.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 5 19.99 Cl 1 17.00 S 80 16.00 P 5 15.00 O 2760 8.00 N 2550 7.00 C 10905 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: 4.03 Conformation dependent library (CDL) restraints added in 2.1 seconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 5 sheets defined 71.5% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'B' and resid 6 through 10 removed outlier: 3.637A pdb=" N ALA B 10 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 20 removed outlier: 4.004A pdb=" N LEU B 20 " --> pdb=" O SER B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.616A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 72 Processing helix chain 'B' and resid 75 through 99 Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 118 through 144 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.681A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.979A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.751A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.638A pdb=" N ALA C 10 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 20 removed outlier: 4.004A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 27 through 53 removed outlier: 5.616A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 72 Processing helix chain 'C' and resid 75 through 99 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.681A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.979A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.751A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.637A pdb=" N ALA A 10 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 20 removed outlier: 4.004A pdb=" N LEU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.616A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 Processing helix chain 'A' and resid 75 through 99 Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 118 through 144 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.681A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.979A pdb=" N VAL A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.751A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'D' and resid 6 through 10 removed outlier: 3.637A pdb=" N ALA D 10 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 20 removed outlier: 4.004A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.616A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 72 Processing helix chain 'D' and resid 75 through 99 Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 118 through 144 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.680A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.978A pdb=" N VAL D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.751A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 324 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'E' and resid 6 through 10 removed outlier: 3.637A pdb=" N ALA E 10 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 20 removed outlier: 4.004A pdb=" N LEU E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 27 through 53 removed outlier: 5.616A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 72 Processing helix chain 'E' and resid 75 through 99 Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.681A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.979A pdb=" N VAL E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.750A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 Processing helix chain 'E' and resid 351 through 355 Processing sheet with id=AA1, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.494A pdb=" N TYR B 347 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 375 through 376 removed outlier: 4.487A pdb=" N TYR C 347 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 375 through 376 removed outlier: 4.489A pdb=" N TYR D 347 " --> pdb=" O GLN C 376 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 348 removed outlier: 4.479A pdb=" N TYR A 347 " --> pdb=" O GLN E 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 375 through 376 removed outlier: 4.484A pdb=" N TYR E 347 " --> pdb=" O GLN D 376 " (cutoff:3.500A) 975 hydrogen bonds defined for protein. 2850 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: 4.91 Time building geometry restraints manager: 4.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2420 1.31 - 1.43: 4840 1.43 - 1.56: 9330 1.56 - 1.68: 10 1.68 - 1.81: 135 Bond restraints: 16735 Sorted by residual: bond pdb=" C11 MC3 A 604 " pdb=" O3 MC3 A 604 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C11 MC3 B 603 " pdb=" O3 MC3 B 603 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C11 MC3 C 603 " pdb=" O3 MC3 C 603 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C11 MC3 E 604 " pdb=" O3 MC3 E 604 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C11 MC3 D 603 " pdb=" O3 MC3 D 603 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 16730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 22438 4.41 - 8.82: 97 8.82 - 13.23: 15 13.23 - 17.64: 5 17.64 - 22.05: 5 Bond angle restraints: 22560 Sorted by residual: angle pdb=" C41 MC3 E 606 " pdb=" C42 MC3 E 606 " pdb=" C43 MC3 E 606 " ideal model delta sigma weight residual 113.45 91.40 22.05 3.00e+00 1.11e-01 5.40e+01 angle pdb=" C41 MC3 A 606 " pdb=" C42 MC3 A 606 " pdb=" C43 MC3 A 606 " ideal model delta sigma weight residual 113.45 91.40 22.05 3.00e+00 1.11e-01 5.40e+01 angle pdb=" C41 MC3 B 605 " pdb=" C42 MC3 B 605 " pdb=" C43 MC3 B 605 " ideal model delta sigma weight residual 113.45 91.42 22.03 3.00e+00 1.11e-01 5.39e+01 angle pdb=" C41 MC3 D 605 " pdb=" C42 MC3 D 605 " pdb=" C43 MC3 D 605 " ideal model delta sigma weight residual 113.45 91.42 22.03 3.00e+00 1.11e-01 5.39e+01 angle pdb=" C41 MC3 C 605 " pdb=" C42 MC3 C 605 " pdb=" C43 MC3 C 605 " ideal model delta sigma weight residual 113.45 91.43 22.02 3.00e+00 1.11e-01 5.39e+01 ... (remaining 22555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.43: 9220 26.43 - 52.87: 575 52.87 - 79.30: 120 79.30 - 105.74: 15 105.74 - 132.17: 5 Dihedral angle restraints: 9935 sinusoidal: 4370 harmonic: 5565 Sorted by residual: dihedral pdb=" C33 MC3 A 604 " pdb=" C31 MC3 A 604 " pdb=" C32 MC3 A 604 " pdb=" O2 MC3 A 604 " ideal model delta sinusoidal sigma weight residual 175.52 43.35 132.17 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C33 MC3 E 604 " pdb=" C31 MC3 E 604 " pdb=" C32 MC3 E 604 " pdb=" O2 MC3 E 604 " ideal model delta sinusoidal sigma weight residual 175.52 43.35 132.17 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C33 MC3 D 603 " pdb=" C31 MC3 D 603 " pdb=" C32 MC3 D 603 " pdb=" O2 MC3 D 603 " ideal model delta sinusoidal sigma weight residual 175.52 43.35 132.17 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 9932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1612 0.034 - 0.067: 566 0.067 - 0.101: 120 0.101 - 0.134: 73 0.134 - 0.168: 14 Chirality restraints: 2385 Sorted by residual: chirality pdb=" CA LEU D 138 " pdb=" N LEU D 138 " pdb=" C LEU D 138 " pdb=" CB LEU D 138 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA LEU B 138 " pdb=" N LEU B 138 " pdb=" C LEU B 138 " pdb=" CB LEU B 138 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA LEU A 138 " pdb=" N LEU A 138 " pdb=" C LEU A 138 " pdb=" CB LEU A 138 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 2382 not shown) Planarity restraints: 2770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 276 " -0.007 2.00e-02 2.50e+03 1.13e-02 2.24e+00 pdb=" CG PHE A 276 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 276 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 276 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 276 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 276 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 276 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 276 " 0.007 2.00e-02 2.50e+03 1.12e-02 2.20e+00 pdb=" CG PHE D 276 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE D 276 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE D 276 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 276 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 276 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 276 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 276 " -0.007 2.00e-02 2.50e+03 1.12e-02 2.19e+00 pdb=" CG PHE E 276 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE E 276 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE E 276 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE E 276 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 276 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 276 " -0.000 2.00e-02 2.50e+03 ... (remaining 2767 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2755 2.76 - 3.29: 15746 3.29 - 3.83: 29403 3.83 - 4.36: 36232 4.36 - 4.90: 59185 Nonbonded interactions: 143321 Sorted by model distance: nonbonded pdb=" NH2 ARG E 51 " pdb=" OD2 ASP E 270 " model vdw 2.222 3.120 nonbonded pdb=" NH2 ARG A 51 " pdb=" OD2 ASP A 270 " model vdw 2.222 3.120 nonbonded pdb=" NH2 ARG C 51 " pdb=" OD2 ASP C 270 " model vdw 2.222 3.120 nonbonded pdb=" NH2 ARG B 51 " pdb=" OD2 ASP B 270 " model vdw 2.222 3.120 nonbonded pdb=" NH2 ARG D 51 " pdb=" OD2 ASP D 270 " model vdw 2.223 3.120 ... (remaining 143316 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 2 through 377 or resid 603 or (resid 604 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42)) or (resid 605 through 606 and \ (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C \ 39 or name C40 or name C41 or name C42 or name C43 or name C44)) or (resid 607 t \ hrough 608 and (name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C42)) or resid 609)) selection = (chain 'B' and (resid 2 through 377 or (resid 603 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 604 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42)) or (resid 605 through 606 and (name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42 or name C43 or name C44)) or (resid 607 through 608 and \ (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C40 or name C41 or name C42)) or (resid 609 and (name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'C' and (resid 2 through 377 or (resid 603 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 604 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42)) or (resid 605 through 606 and (name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42 or name C43 or name C44)) or (resid 607 through 608 and \ (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C40 or name C41 or name C42)) or (resid 609 and (name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'D' and (resid 2 through 377 or (resid 603 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 604 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42)) or (resid 605 through 606 and (name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42 or name C43 or name C44)) or (resid 607 through 608 and \ (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C40 or name C41 or name C42)) or (resid 609 and (name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'E' and (resid 2 through 377 or resid 603 or (resid 604 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42)) or (resid 605 through 606 and \ (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C \ 39 or name C40 or name C41 or name C42 or name C43 or name C44)) or (resid 607 t \ hrough 608 and (name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C42)) or resid 609)) } 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 37.400 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16735 Z= 0.327 Angle : 0.943 22.051 22560 Z= 0.406 Chirality : 0.040 0.168 2385 Planarity : 0.004 0.024 2770 Dihedral : 17.688 132.174 6345 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.18 % Allowed : 9.14 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.19), residues: 1870 helix: 1.54 (0.15), residues: 1235 sheet: None (None), residues: 0 loop : 0.59 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 309 HIS 0.005 0.002 HIS E 178 PHE 0.025 0.002 PHE A 276 TYR 0.022 0.001 TYR C 97 ARG 0.003 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 1.747 Fit side-chains REVERT: C 193 MET cc_start: 0.9014 (tpt) cc_final: 0.8762 (tpp) REVERT: A 68 TYR cc_start: 0.6613 (t80) cc_final: 0.6399 (t80) REVERT: A 193 MET cc_start: 0.8984 (tpt) cc_final: 0.8757 (tpp) REVERT: A 370 LYS cc_start: 0.8620 (ttpt) cc_final: 0.8368 (tttm) REVERT: D 276 PHE cc_start: 0.7633 (t80) cc_final: 0.7334 (m-80) REVERT: D 370 LYS cc_start: 0.8637 (ttpt) cc_final: 0.8148 (ttpp) REVERT: E 276 PHE cc_start: 0.7694 (t80) cc_final: 0.7459 (m-80) REVERT: E 370 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8400 (ttpp) outliers start: 20 outliers final: 7 residues processed: 231 average time/residue: 1.5139 time to fit residues: 384.5509 Evaluate side-chains 190 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 183 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain E residue 178 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 0.0970 chunk 145 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16735 Z= 0.170 Angle : 0.507 8.102 22560 Z= 0.264 Chirality : 0.038 0.150 2385 Planarity : 0.004 0.029 2770 Dihedral : 13.619 127.246 2654 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.65 % Allowed : 10.32 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.19), residues: 1870 helix: 1.77 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.39 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 309 HIS 0.004 0.001 HIS E 178 PHE 0.017 0.001 PHE E 276 TYR 0.018 0.002 TYR B 68 ARG 0.005 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 1.743 Fit side-chains REVERT: B 119 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: B 372 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7994 (mt-10) REVERT: C 119 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: C 193 MET cc_start: 0.8986 (tpt) cc_final: 0.8762 (tpp) REVERT: C 276 PHE cc_start: 0.7978 (m-80) cc_final: 0.7202 (t80) REVERT: C 372 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8200 (mt-10) REVERT: A 68 TYR cc_start: 0.6225 (t80) cc_final: 0.5782 (t80) REVERT: A 193 MET cc_start: 0.8934 (tpt) cc_final: 0.8684 (tpp) REVERT: A 276 PHE cc_start: 0.7917 (m-10) cc_final: 0.7412 (t80) REVERT: A 370 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8485 (tttm) REVERT: D 119 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7000 (tp30) REVERT: D 370 LYS cc_start: 0.8787 (ttpt) cc_final: 0.8457 (ttpp) REVERT: D 372 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7998 (mt-10) REVERT: E 119 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: E 276 PHE cc_start: 0.7665 (t80) cc_final: 0.7434 (m-80) REVERT: E 370 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8342 (ttpp) outliers start: 28 outliers final: 15 residues processed: 221 average time/residue: 1.5117 time to fit residues: 369.4459 Evaluate side-chains 208 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 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 : 0.003 0.031 16735 Z= 0.195 Angle : 0.504 7.508 22560 Z= 0.264 Chirality : 0.039 0.150 2385 Planarity : 0.004 0.033 2770 Dihedral : 12.757 121.601 2650 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.36 % Allowed : 10.38 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.19), residues: 1870 helix: 1.80 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : 0.46 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 309 HIS 0.004 0.001 HIS D 326 PHE 0.016 0.001 PHE C 248 TYR 0.020 0.002 TYR E 97 ARG 0.005 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 1.753 Fit side-chains REVERT: B 119 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: C 119 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: C 193 MET cc_start: 0.8987 (tpt) cc_final: 0.8764 (tpp) REVERT: C 276 PHE cc_start: 0.7954 (m-80) cc_final: 0.7202 (t80) REVERT: A 276 PHE cc_start: 0.7875 (m-10) cc_final: 0.7388 (t80) REVERT: A 370 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8463 (tttm) REVERT: D 119 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.6993 (tp30) REVERT: D 370 LYS cc_start: 0.8799 (ttpt) cc_final: 0.8521 (ttpp) REVERT: E 51 ARG cc_start: 0.8035 (mmt-90) cc_final: 0.7591 (mmt180) REVERT: E 119 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7074 (tp30) REVERT: E 276 PHE cc_start: 0.7756 (t80) cc_final: 0.7491 (m-80) outliers start: 40 outliers final: 16 residues processed: 235 average time/residue: 1.5203 time to fit residues: 392.9351 Evaluate side-chains 221 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.6980 chunk 126 optimal weight: 0.3980 chunk 87 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 160 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16735 Z= 0.203 Angle : 0.507 7.360 22560 Z= 0.265 Chirality : 0.039 0.149 2385 Planarity : 0.004 0.034 2770 Dihedral : 12.213 119.334 2650 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.95 % Allowed : 10.97 % Favored : 87.08 % 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: 1.94 (0.19), residues: 1870 helix: 1.81 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : 0.43 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 309 HIS 0.004 0.001 HIS D 326 PHE 0.019 0.001 PHE A 80 TYR 0.020 0.002 TYR E 97 ARG 0.006 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 1.846 Fit side-chains REVERT: B 119 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7671 (tp30) REVERT: B 262 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7807 (mmmt) REVERT: C 119 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: C 193 MET cc_start: 0.8989 (tpt) cc_final: 0.8761 (tpp) REVERT: A 276 PHE cc_start: 0.7863 (m-10) cc_final: 0.7390 (t80) REVERT: A 370 LYS cc_start: 0.8703 (ttpt) cc_final: 0.8440 (tttm) REVERT: D 119 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7073 (tp30) REVERT: D 370 LYS cc_start: 0.8799 (ttpt) cc_final: 0.8509 (ttpp) REVERT: D 371 GLU cc_start: 0.7923 (mp0) cc_final: 0.7720 (mp0) REVERT: E 51 ARG cc_start: 0.8002 (mmt-90) cc_final: 0.7586 (mmt180) outliers start: 33 outliers final: 17 residues processed: 235 average time/residue: 1.5706 time to fit residues: 404.4676 Evaluate side-chains 222 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 0.0070 chunk 101 optimal weight: 0.0060 chunk 2 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 73 optimal weight: 0.1980 chunk 152 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 chunk 160 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 overall best weight: 0.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 HIS ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16735 Z= 0.130 Angle : 0.459 6.930 22560 Z= 0.236 Chirality : 0.036 0.147 2385 Planarity : 0.004 0.031 2770 Dihedral : 11.572 115.174 2648 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.77 % Allowed : 11.68 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.98 (0.19), residues: 1870 helix: 1.87 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : 0.37 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 93 HIS 0.003 0.001 HIS A 178 PHE 0.014 0.001 PHE D 80 TYR 0.015 0.001 TYR C 68 ARG 0.006 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 1.930 Fit side-chains REVERT: C 119 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: A 276 PHE cc_start: 0.7792 (m-10) cc_final: 0.7366 (t80) REVERT: A 370 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8392 (tttm) REVERT: D 119 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7025 (tp30) REVERT: D 370 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8516 (ttpp) REVERT: E 370 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8367 (ttpp) outliers start: 30 outliers final: 13 residues processed: 230 average time/residue: 1.5334 time to fit residues: 387.9001 Evaluate side-chains 217 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 178 optimal weight: 0.7980 chunk 148 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 : 0.003 0.032 16735 Z= 0.205 Angle : 0.505 6.997 22560 Z= 0.262 Chirality : 0.039 0.151 2385 Planarity : 0.004 0.035 2770 Dihedral : 11.458 113.863 2646 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.65 % Allowed : 12.27 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.19), residues: 1870 helix: 1.88 (0.15), residues: 1215 sheet: None (None), residues: 0 loop : 0.39 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 309 HIS 0.004 0.001 HIS B 178 PHE 0.018 0.001 PHE C 248 TYR 0.021 0.002 TYR A 97 ARG 0.007 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 1.867 Fit side-chains REVERT: B 262 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7673 (mmmt) REVERT: C 119 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: C 276 PHE cc_start: 0.7774 (m-80) cc_final: 0.7205 (t80) REVERT: A 276 PHE cc_start: 0.7842 (m-10) cc_final: 0.7379 (t80) REVERT: A 370 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8427 (tttm) REVERT: D 119 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7129 (tp30) REVERT: D 370 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8489 (ttpp) outliers start: 28 outliers final: 14 residues processed: 215 average time/residue: 1.5478 time to fit residues: 365.6448 Evaluate side-chains 218 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 111 optimal weight: 0.0040 chunk 108 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16735 Z= 0.179 Angle : 0.494 7.240 22560 Z= 0.254 Chirality : 0.038 0.150 2385 Planarity : 0.004 0.034 2770 Dihedral : 11.183 113.542 2644 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.59 % Allowed : 12.04 % Favored : 86.37 % 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: 1.98 (0.19), residues: 1870 helix: 1.89 (0.15), residues: 1210 sheet: None (None), residues: 0 loop : 0.32 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 309 HIS 0.004 0.001 HIS E 178 PHE 0.016 0.001 PHE C 248 TYR 0.019 0.001 TYR A 97 ARG 0.007 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 1.812 Fit side-chains REVERT: B 119 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7637 (tp30) REVERT: B 262 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7689 (mmmt) REVERT: C 119 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: C 276 PHE cc_start: 0.7748 (m-80) cc_final: 0.7213 (t80) REVERT: A 276 PHE cc_start: 0.7848 (m-10) cc_final: 0.7385 (t80) REVERT: A 370 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8419 (tttm) REVERT: D 119 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7137 (tp30) REVERT: D 370 LYS cc_start: 0.8762 (ttpt) cc_final: 0.8474 (ttpp) REVERT: E 51 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.5842 (mpt180) outliers start: 27 outliers final: 15 residues processed: 216 average time/residue: 1.5853 time to fit residues: 374.8145 Evaluate side-chains 218 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16735 Z= 0.205 Angle : 0.517 7.552 22560 Z= 0.266 Chirality : 0.039 0.164 2385 Planarity : 0.004 0.045 2770 Dihedral : 11.085 113.915 2644 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.42 % Allowed : 12.33 % Favored : 86.25 % 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: 1.94 (0.19), residues: 1870 helix: 1.84 (0.15), residues: 1215 sheet: None (None), residues: 0 loop : 0.34 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 309 HIS 0.004 0.001 HIS E 178 PHE 0.019 0.001 PHE C 248 TYR 0.021 0.002 TYR A 97 ARG 0.009 0.000 ARG C 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 2.052 Fit side-chains REVERT: B 119 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7643 (tp30) REVERT: B 262 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7706 (mmmt) REVERT: B 370 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8354 (ttpp) REVERT: C 119 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: C 276 PHE cc_start: 0.7753 (m-80) cc_final: 0.7206 (t80) REVERT: A 276 PHE cc_start: 0.7864 (m-10) cc_final: 0.7391 (t80) REVERT: A 370 LYS cc_start: 0.8672 (ttpt) cc_final: 0.8416 (tttm) REVERT: D 119 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7207 (tp30) REVERT: D 370 LYS cc_start: 0.8759 (ttpt) cc_final: 0.8471 (ttpp) REVERT: E 51 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.5808 (mpt180) outliers start: 24 outliers final: 15 residues processed: 211 average time/residue: 1.6091 time to fit residues: 372.6483 Evaluate side-chains 216 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 166 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16735 Z= 0.184 Angle : 0.510 9.374 22560 Z= 0.260 Chirality : 0.039 0.252 2385 Planarity : 0.004 0.047 2770 Dihedral : 10.903 113.396 2644 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.42 % Allowed : 12.39 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.92 (0.19), residues: 1870 helix: 1.85 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.29 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 309 HIS 0.004 0.001 HIS E 178 PHE 0.017 0.001 PHE C 248 TYR 0.020 0.001 TYR A 97 ARG 0.009 0.000 ARG C 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 1.887 Fit side-chains REVERT: B 119 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7644 (tp30) REVERT: B 262 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7728 (mmmt) REVERT: B 370 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8374 (ttpp) REVERT: C 119 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: C 276 PHE cc_start: 0.7759 (m-80) cc_final: 0.7211 (t80) REVERT: A 276 PHE cc_start: 0.7858 (m-10) cc_final: 0.7393 (t80) REVERT: A 370 LYS cc_start: 0.8664 (ttpt) cc_final: 0.8422 (tttm) REVERT: D 119 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7198 (tp30) REVERT: D 370 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8474 (ttpp) REVERT: E 51 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.5983 (mpt180) outliers start: 24 outliers final: 15 residues processed: 213 average time/residue: 1.5974 time to fit residues: 373.1787 Evaluate side-chains 215 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 184 optimal weight: 7.9990 chunk 169 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 15 optimal weight: 0.0010 chunk 113 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16735 Z= 0.232 Angle : 0.546 10.684 22560 Z= 0.279 Chirality : 0.041 0.254 2385 Planarity : 0.004 0.048 2770 Dihedral : 10.936 114.282 2644 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.30 % Allowed : 12.45 % Favored : 86.25 % 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: 1.88 (0.19), residues: 1870 helix: 1.79 (0.15), residues: 1215 sheet: None (None), residues: 0 loop : 0.33 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 309 HIS 0.004 0.001 HIS E 178 PHE 0.021 0.001 PHE B 248 TYR 0.022 0.002 TYR A 97 ARG 0.009 0.000 ARG C 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 1.734 Fit side-chains REVERT: B 119 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7655 (tp30) REVERT: B 262 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7842 (mmmt) REVERT: C 119 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: C 276 PHE cc_start: 0.7772 (m-80) cc_final: 0.7204 (t80) REVERT: A 276 PHE cc_start: 0.7905 (m-10) cc_final: 0.7400 (t80) REVERT: A 370 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8423 (tttm) REVERT: D 119 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7237 (tp30) REVERT: D 370 LYS cc_start: 0.8756 (ttpt) cc_final: 0.8496 (ttpp) REVERT: D 371 GLU cc_start: 0.7966 (mp0) cc_final: 0.7747 (mp0) outliers start: 22 outliers final: 16 residues processed: 209 average time/residue: 1.5869 time to fit residues: 362.7826 Evaluate side-chains 218 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.081009 restraints weight = 19735.350| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.63 r_work: 0.2894 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16735 Z= 0.179 Angle : 0.519 11.063 22560 Z= 0.262 Chirality : 0.040 0.254 2385 Planarity : 0.004 0.047 2770 Dihedral : 10.594 113.631 2644 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.30 % Allowed : 12.68 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.19), residues: 1870 helix: 1.81 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.27 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 309 HIS 0.003 0.001 HIS E 178 PHE 0.017 0.001 PHE D 80 TYR 0.019 0.001 TYR A 97 ARG 0.009 0.000 ARG C 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6351.45 seconds wall clock time: 115 minutes 37.43 seconds (6937.43 seconds total)