Starting phenix.real_space_refine on Wed Mar 4 21:13:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d1l_27134/03_2026/8d1l_27134.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1l_27134/03_2026/8d1l_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 { model { file = "/net/cci-nas-00/data/ceres_data/8d1l_27134/03_2026/8d1l_27134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1l_27134/03_2026/8d1l_27134.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d1l_27134/03_2026/8d1l_27134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1l_27134/03_2026/8d1l_27134.map" } resolution = 2.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16306 Number of models: 1 Model: "" Number of chains: 10 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: "C" 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: "D" 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: "E" 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-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 41 Chain: "C" 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-1': 6, 'MC3:plan-2': 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-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 41 Chain: "D" 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-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 41 Chain: "E" 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-1': 6, 'MC3:plan-2': 6} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 3.59, per 1000 atoms: 0.22 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: 1.46 Conformation dependent library (CDL) restraints added in 479.3 milliseconds 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: 0.31 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: 2.69 Time building geometry restraints manager: 1.83 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: 5.800 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.120 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.290 ------------------------------------------------------------------------------- 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= 0.241 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 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 ARG 0.003 0.000 ARG A 130 TYR 0.022 0.001 TYR C 97 PHE 0.025 0.002 PHE A 276 TRP 0.012 0.002 TRP D 309 HIS 0.005 0.002 HIS E 178 Details of bonding type rmsd covalent geometry : bond 0.00497 (16735) covalent geometry : angle 0.94349 (22560) hydrogen bonds : bond 0.13205 ( 975) hydrogen bonds : angle 5.21751 ( 2850) *********************** 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 : 0.659 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: 0.6923 time to fit residues: 174.9868 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 : 0.582 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.111603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.080722 restraints weight = 20162.420| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.66 r_work: 0.2865 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1147 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= 0.144 Angle : 0.527 8.331 22560 Z= 0.275 Chirality : 0.039 0.151 2385 Planarity : 0.004 0.030 2770 Dihedral : 13.679 127.453 2654 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.83 % Allowed : 10.38 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.19), residues: 1870 helix: 1.77 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.41 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 25 TYR 0.019 0.002 TYR E 97 PHE 0.019 0.001 PHE E 276 TRP 0.013 0.002 TRP B 309 HIS 0.004 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00314 (16735) covalent geometry : angle 0.52748 (22560) hydrogen bonds : bond 0.05976 ( 975) hydrogen bonds : angle 4.36982 ( 2850) *********************** 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 233 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.619 Fit side-chains REVERT: B 72 TYR cc_start: 0.6606 (m-80) cc_final: 0.6301 (m-80) REVERT: B 119 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: B 369 ASN cc_start: 0.7161 (m110) cc_final: 0.6202 (p0) REVERT: C 119 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: C 193 MET cc_start: 0.8868 (tpt) cc_final: 0.8547 (tpp) REVERT: C 276 PHE cc_start: 0.7909 (m-80) cc_final: 0.6428 (t80) REVERT: C 369 ASN cc_start: 0.6722 (m110) cc_final: 0.6194 (p0) REVERT: C 372 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7654 (mt-10) REVERT: A 68 TYR cc_start: 0.5323 (t80) cc_final: 0.4795 (t80) REVERT: A 276 PHE cc_start: 0.7895 (m-10) cc_final: 0.6673 (t80) REVERT: A 369 ASN cc_start: 0.7036 (m110) cc_final: 0.6539 (p0) REVERT: A 370 LYS cc_start: 0.7931 (ttpt) cc_final: 0.7441 (tttm) REVERT: A 372 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7369 (mt-10) REVERT: D 119 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7336 (tp30) REVERT: D 194 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8293 (ttpp) REVERT: D 276 PHE cc_start: 0.7318 (t80) cc_final: 0.7102 (t80) REVERT: D 369 ASN cc_start: 0.6769 (OUTLIER) cc_final: 0.6174 (p0) REVERT: D 370 LYS cc_start: 0.7974 (ttpt) cc_final: 0.7348 (ttpp) REVERT: D 372 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7415 (mt-10) REVERT: E 61 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7328 (mmp) REVERT: E 119 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: E 276 PHE cc_start: 0.7495 (t80) cc_final: 0.6797 (m-80) REVERT: E 369 ASN cc_start: 0.6827 (m110) cc_final: 0.6459 (p0) REVERT: E 370 LYS cc_start: 0.7886 (ttpt) cc_final: 0.7355 (ttpp) REVERT: E 373 MET cc_start: 0.8195 (mtp) cc_final: 0.7982 (mtm) outliers start: 31 outliers final: 16 residues processed: 224 average time/residue: 0.6509 time to fit residues: 160.0402 Evaluate side-chains 215 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 SER 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 D residue 369 ASN Chi-restraints excluded: chain E residue 61 MET 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 94 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 0.0170 chunk 172 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.113233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.082391 restraints weight = 20264.440| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.66 r_work: 0.2895 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1412 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= 0.125 Angle : 0.485 7.375 22560 Z= 0.253 Chirality : 0.038 0.149 2385 Planarity : 0.004 0.034 2770 Dihedral : 12.564 120.819 2650 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.42 % Allowed : 10.38 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.19), residues: 1870 helix: 1.82 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : 0.45 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 51 TYR 0.018 0.001 TYR E 97 PHE 0.015 0.001 PHE D 80 TRP 0.011 0.001 TRP B 309 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00263 (16735) covalent geometry : angle 0.48457 (22560) hydrogen bonds : bond 0.05533 ( 975) hydrogen bonds : angle 4.21264 ( 2850) *********************** 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 257 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 0.606 Fit side-chains REVERT: B 119 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: B 355 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7720 (ttt180) REVERT: C 119 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: C 193 MET cc_start: 0.8857 (tpt) cc_final: 0.8545 (tpp) REVERT: C 355 ARG cc_start: 0.8052 (ttp-170) cc_final: 0.7763 (ttt90) REVERT: C 369 ASN cc_start: 0.6814 (m110) cc_final: 0.6150 (p0) REVERT: C 372 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7610 (mt-10) REVERT: A 193 MET cc_start: 0.8823 (tpt) cc_final: 0.8525 (tpp) REVERT: A 276 PHE cc_start: 0.7888 (m-10) cc_final: 0.6662 (t80) REVERT: A 369 ASN cc_start: 0.6950 (OUTLIER) cc_final: 0.6400 (p0) REVERT: A 370 LYS cc_start: 0.7991 (ttpt) cc_final: 0.7453 (tttm) REVERT: A 372 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7335 (mt-10) REVERT: D 57 GLU cc_start: 0.7681 (mp0) cc_final: 0.7245 (pm20) REVERT: D 119 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7340 (tp30) REVERT: D 194 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8292 (ttpp) REVERT: D 276 PHE cc_start: 0.7483 (t80) cc_final: 0.7202 (t80) REVERT: D 282 PHE cc_start: 0.7628 (m-80) cc_final: 0.7349 (m-80) REVERT: D 355 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7711 (ttt180) REVERT: D 369 ASN cc_start: 0.6729 (OUTLIER) cc_final: 0.6112 (p0) REVERT: D 370 LYS cc_start: 0.8061 (ttpt) cc_final: 0.7423 (ttpp) REVERT: D 372 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7248 (mt-10) REVERT: E 51 ARG cc_start: 0.7989 (mmt-90) cc_final: 0.7466 (mmt180) REVERT: E 61 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7305 (mmp) REVERT: E 119 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7415 (tp30) REVERT: E 163 MET cc_start: 0.8954 (ttp) cc_final: 0.8705 (ttm) REVERT: E 276 PHE cc_start: 0.7564 (t80) cc_final: 0.7261 (t80) REVERT: E 369 ASN cc_start: 0.6734 (m110) cc_final: 0.6259 (p0) REVERT: E 370 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7338 (ttpp) REVERT: E 372 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7604 (mt-10) outliers start: 41 outliers final: 17 residues processed: 240 average time/residue: 0.6874 time to fit residues: 180.7859 Evaluate side-chains 235 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 A residue 369 ASN 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 D residue 369 ASN Chi-restraints excluded: chain E residue 61 MET 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 205 ILE 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 17 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.107616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.076303 restraints weight = 20428.875| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.67 r_work: 0.2793 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 16735 Z= 0.284 Angle : 0.621 8.373 22560 Z= 0.326 Chirality : 0.047 0.164 2385 Planarity : 0.005 0.038 2770 Dihedral : 12.847 122.956 2650 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.48 % Allowed : 10.03 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.19), residues: 1870 helix: 1.52 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : 0.17 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 51 TYR 0.029 0.002 TYR E 97 PHE 0.031 0.002 PHE C 248 TRP 0.019 0.002 TRP C 309 HIS 0.007 0.002 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00677 (16735) covalent geometry : angle 0.62050 (22560) hydrogen bonds : bond 0.07251 ( 975) hydrogen bonds : angle 4.55134 ( 2850) *********************** 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 244 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.606 Fit side-chains REVERT: B 119 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7942 (tp30) REVERT: B 262 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6982 (mmmt) REVERT: B 374 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7386 (mm-30) REVERT: C 119 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: C 193 MET cc_start: 0.8851 (tpt) cc_final: 0.8513 (tpp) REVERT: A 276 PHE cc_start: 0.7911 (m-10) cc_final: 0.6600 (t80) REVERT: A 369 ASN cc_start: 0.7024 (OUTLIER) cc_final: 0.6385 (p0) REVERT: A 370 LYS cc_start: 0.7996 (ttpt) cc_final: 0.7479 (tttm) REVERT: A 371 GLU cc_start: 0.7562 (mp0) cc_final: 0.7323 (mp0) REVERT: A 372 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7552 (mt-10) REVERT: D 57 GLU cc_start: 0.7720 (mp0) cc_final: 0.7285 (pm20) REVERT: D 119 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7432 (tp30) REVERT: D 194 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8315 (ttpp) REVERT: D 276 PHE cc_start: 0.7542 (t80) cc_final: 0.7257 (t80) REVERT: D 355 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7415 (ttt180) REVERT: D 369 ASN cc_start: 0.6771 (m110) cc_final: 0.6378 (p0) REVERT: D 370 LYS cc_start: 0.8023 (ttpt) cc_final: 0.7431 (ttpp) REVERT: E 51 ARG cc_start: 0.7976 (mmt-90) cc_final: 0.7533 (mmt180) REVERT: E 61 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7330 (mmp) REVERT: E 119 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7501 (tp30) REVERT: E 276 PHE cc_start: 0.7607 (t80) cc_final: 0.6819 (m-80) REVERT: E 370 LYS cc_start: 0.7915 (ttpt) cc_final: 0.7349 (ttpp) outliers start: 42 outliers final: 20 residues processed: 227 average time/residue: 0.7106 time to fit residues: 176.5832 Evaluate side-chains 233 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 B residue 374 GLU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 369 ASN 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 D residue 355 ARG Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 76 ILE 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 205 ILE 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 80 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.112015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.081126 restraints weight = 20277.394| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.67 r_work: 0.2875 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16735 Z= 0.133 Angle : 0.503 7.384 22560 Z= 0.261 Chirality : 0.038 0.149 2385 Planarity : 0.004 0.034 2770 Dihedral : 12.103 119.660 2648 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.01 % Allowed : 11.21 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.19), residues: 1870 helix: 1.75 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.37 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 51 TYR 0.019 0.002 TYR E 97 PHE 0.016 0.001 PHE C 276 TRP 0.014 0.002 TRP B 309 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00287 (16735) covalent geometry : angle 0.50262 (22560) hydrogen bonds : bond 0.05675 ( 975) hydrogen bonds : angle 4.29592 ( 2850) *********************** 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 246 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.672 Fit side-chains REVERT: B 72 TYR cc_start: 0.6411 (m-80) cc_final: 0.6209 (m-80) REVERT: B 119 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7873 (tp30) REVERT: C 119 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: C 193 MET cc_start: 0.8868 (tpt) cc_final: 0.8569 (tpp) REVERT: C 259 ASN cc_start: 0.7326 (t0) cc_final: 0.6851 (t0) REVERT: C 276 PHE cc_start: 0.7895 (m-80) cc_final: 0.6506 (t80) REVERT: C 355 ARG cc_start: 0.8061 (ttp-170) cc_final: 0.7632 (ttt90) REVERT: A 193 MET cc_start: 0.8829 (tpt) cc_final: 0.8539 (tpp) REVERT: A 276 PHE cc_start: 0.7841 (m-10) cc_final: 0.6637 (t80) REVERT: A 369 ASN cc_start: 0.6916 (OUTLIER) cc_final: 0.6194 (p0) REVERT: A 370 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7368 (tttm) REVERT: A 371 GLU cc_start: 0.7629 (mp0) cc_final: 0.7340 (mp0) REVERT: A 372 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7315 (mt-10) REVERT: D 57 GLU cc_start: 0.7739 (mp0) cc_final: 0.7352 (pm20) REVERT: D 72 TYR cc_start: 0.6444 (m-80) cc_final: 0.6187 (m-80) REVERT: D 119 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7417 (tp30) REVERT: D 194 LYS cc_start: 0.8544 (ttmt) cc_final: 0.8279 (ttpp) REVERT: D 276 PHE cc_start: 0.7525 (t80) cc_final: 0.7241 (t80) REVERT: D 355 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7414 (ttt180) REVERT: D 369 ASN cc_start: 0.6716 (OUTLIER) cc_final: 0.6311 (p0) REVERT: D 370 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7582 (ttpp) REVERT: E 51 ARG cc_start: 0.7909 (mmt-90) cc_final: 0.7608 (mpt90) REVERT: E 61 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7296 (mmp) REVERT: E 119 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7454 (tp30) REVERT: E 276 PHE cc_start: 0.7538 (t80) cc_final: 0.6766 (m-80) REVERT: E 369 ASN cc_start: 0.6850 (m110) cc_final: 0.6317 (p0) REVERT: E 370 LYS cc_start: 0.7901 (ttpt) cc_final: 0.7338 (ttpp) outliers start: 34 outliers final: 17 residues processed: 232 average time/residue: 0.6877 time to fit residues: 174.5756 Evaluate side-chains 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 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 A residue 369 ASN Chi-restraints excluded: chain D residue 75 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 D residue 355 ARG Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain E residue 61 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.078720 restraints weight = 20263.165| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.66 r_work: 0.2834 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 : 0.004 0.037 16735 Z= 0.179 Angle : 0.543 7.399 22560 Z= 0.283 Chirality : 0.041 0.154 2385 Planarity : 0.004 0.036 2770 Dihedral : 12.046 118.898 2646 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.89 % Allowed : 11.62 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.19), residues: 1870 helix: 1.76 (0.15), residues: 1210 sheet: None (None), residues: 0 loop : 0.34 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 51 TYR 0.024 0.002 TYR E 97 PHE 0.021 0.002 PHE A 248 TRP 0.016 0.002 TRP B 309 HIS 0.005 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00411 (16735) covalent geometry : angle 0.54315 (22560) hydrogen bonds : bond 0.06283 ( 975) hydrogen bonds : angle 4.38275 ( 2850) *********************** 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 242 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.617 Fit side-chains REVERT: B 61 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7790 (tpp) REVERT: B 119 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7891 (tp30) REVERT: B 262 LYS cc_start: 0.7378 (mptp) cc_final: 0.7163 (mmmt) REVERT: C 119 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: C 193 MET cc_start: 0.8859 (tpt) cc_final: 0.8552 (tpp) REVERT: C 259 ASN cc_start: 0.7326 (t0) cc_final: 0.6854 (t0) REVERT: C 276 PHE cc_start: 0.7905 (m-80) cc_final: 0.6466 (t80) REVERT: C 355 ARG cc_start: 0.8013 (ttp-170) cc_final: 0.7689 (ttt90) REVERT: A 193 MET cc_start: 0.8823 (tpt) cc_final: 0.8518 (tpp) REVERT: A 276 PHE cc_start: 0.7887 (m-10) cc_final: 0.6643 (t80) REVERT: A 369 ASN cc_start: 0.6810 (OUTLIER) cc_final: 0.6230 (p0) REVERT: A 370 LYS cc_start: 0.7805 (ttpt) cc_final: 0.7240 (tttm) REVERT: A 371 GLU cc_start: 0.7579 (mp0) cc_final: 0.7324 (mp0) REVERT: A 372 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7405 (mt-10) REVERT: D 57 GLU cc_start: 0.7739 (mp0) cc_final: 0.7348 (pm20) REVERT: D 119 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7447 (tp30) REVERT: D 194 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8278 (ttpp) REVERT: D 276 PHE cc_start: 0.7586 (t80) cc_final: 0.7314 (t80) REVERT: D 355 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7400 (ttt180) REVERT: D 369 ASN cc_start: 0.6670 (m110) cc_final: 0.6301 (p0) REVERT: D 370 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7554 (ttpp) REVERT: E 51 ARG cc_start: 0.7952 (mmt-90) cc_final: 0.7492 (mmt180) REVERT: E 61 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7312 (mmp) REVERT: E 119 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7489 (tp30) REVERT: E 276 PHE cc_start: 0.7587 (t80) cc_final: 0.7324 (t80) REVERT: E 369 ASN cc_start: 0.6863 (m110) cc_final: 0.6297 (p0) REVERT: E 370 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7385 (ttpp) outliers start: 32 outliers final: 18 residues processed: 225 average time/residue: 0.7166 time to fit residues: 175.6326 Evaluate side-chains 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 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 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 205 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 369 ASN Chi-restraints excluded: chain D residue 75 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 D residue 355 ARG Chi-restraints excluded: chain E residue 61 MET 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 205 ILE 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 141 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 127 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 111 optimal weight: 0.0000 chunk 156 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 140 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 HIS 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.114039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.083601 restraints weight = 20161.976| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.65 r_work: 0.2918 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16735 Z= 0.110 Angle : 0.478 7.396 22560 Z= 0.245 Chirality : 0.037 0.148 2385 Planarity : 0.004 0.032 2770 Dihedral : 11.338 116.336 2644 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.59 % Allowed : 12.09 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.19), residues: 1870 helix: 1.84 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.32 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 51 TYR 0.015 0.001 TYR B 97 PHE 0.016 0.001 PHE D 80 TRP 0.013 0.001 TRP B 185 HIS 0.003 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00220 (16735) covalent geometry : angle 0.47841 (22560) hydrogen bonds : bond 0.05200 ( 975) hydrogen bonds : angle 4.20704 ( 2850) *********************** 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 243 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.548 Fit side-chains REVERT: B 61 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7754 (tpp) REVERT: B 119 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7868 (tp30) REVERT: B 262 LYS cc_start: 0.7375 (mptp) cc_final: 0.7145 (mmmt) REVERT: B 355 ARG cc_start: 0.7919 (ttm-80) cc_final: 0.7695 (ttt180) REVERT: C 119 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: C 193 MET cc_start: 0.8858 (tpt) cc_final: 0.8568 (tpp) REVERT: C 259 ASN cc_start: 0.7281 (t0) cc_final: 0.6805 (t0) REVERT: C 276 PHE cc_start: 0.7816 (m-80) cc_final: 0.6513 (t80) REVERT: C 355 ARG cc_start: 0.8069 (ttp-170) cc_final: 0.7668 (ttt90) REVERT: C 369 ASN cc_start: 0.6726 (m110) cc_final: 0.6168 (m110) REVERT: C 372 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7348 (mt-10) REVERT: A 193 MET cc_start: 0.8832 (tpt) cc_final: 0.8545 (tpp) REVERT: A 276 PHE cc_start: 0.7838 (m-10) cc_final: 0.6638 (t80) REVERT: A 369 ASN cc_start: 0.6812 (OUTLIER) cc_final: 0.6222 (p0) REVERT: A 370 LYS cc_start: 0.7863 (ttpt) cc_final: 0.7305 (tttm) REVERT: A 371 GLU cc_start: 0.7712 (mp0) cc_final: 0.7336 (mp0) REVERT: A 372 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7299 (mt-10) REVERT: D 57 GLU cc_start: 0.7708 (mp0) cc_final: 0.7352 (pm20) REVERT: D 72 TYR cc_start: 0.6358 (m-80) cc_final: 0.6143 (m-80) REVERT: D 119 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7400 (tp30) REVERT: D 194 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8306 (ttpp) REVERT: D 276 PHE cc_start: 0.7554 (t80) cc_final: 0.7291 (t80) REVERT: D 369 ASN cc_start: 0.6660 (m110) cc_final: 0.6189 (p0) REVERT: D 370 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7556 (ttpp) REVERT: E 51 ARG cc_start: 0.7890 (mmt-90) cc_final: 0.7576 (mpt90) REVERT: E 61 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7281 (mmp) REVERT: E 119 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7442 (tp30) REVERT: E 276 PHE cc_start: 0.7463 (t80) cc_final: 0.7246 (t80) REVERT: E 369 ASN cc_start: 0.6866 (m110) cc_final: 0.6363 (p0) REVERT: E 370 LYS cc_start: 0.7908 (ttpt) cc_final: 0.7347 (ttpp) outliers start: 27 outliers final: 14 residues processed: 231 average time/residue: 0.6885 time to fit residues: 173.9619 Evaluate side-chains 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 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 A residue 369 ASN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 61 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 180 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.111109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.080196 restraints weight = 20318.001| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.66 r_work: 0.2860 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1623 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= 0.152 Angle : 0.524 7.685 22560 Z= 0.270 Chirality : 0.039 0.151 2385 Planarity : 0.004 0.035 2770 Dihedral : 11.364 117.114 2644 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.59 % Allowed : 12.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.19), residues: 1870 helix: 1.80 (0.15), residues: 1215 sheet: None (None), residues: 0 loop : 0.38 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 51 TYR 0.022 0.002 TYR D 97 PHE 0.018 0.001 PHE C 248 TRP 0.015 0.002 TRP A 309 HIS 0.005 0.001 HIS E 178 Details of bonding type rmsd covalent geometry : bond 0.00340 (16735) covalent geometry : angle 0.52426 (22560) hydrogen bonds : bond 0.05887 ( 975) hydrogen bonds : angle 4.30187 ( 2850) *********************** 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 240 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 0.555 Fit side-chains REVERT: B 61 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7776 (tpp) REVERT: B 119 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7882 (tp30) REVERT: B 262 LYS cc_start: 0.7378 (mptp) cc_final: 0.7136 (mmmt) REVERT: B 355 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7715 (ttt180) REVERT: C 119 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: C 193 MET cc_start: 0.8858 (tpt) cc_final: 0.8556 (tpp) REVERT: C 259 ASN cc_start: 0.7305 (t0) cc_final: 0.6824 (t0) REVERT: C 276 PHE cc_start: 0.7824 (m-80) cc_final: 0.6494 (t80) REVERT: C 355 ARG cc_start: 0.8030 (ttp-170) cc_final: 0.7729 (ttt90) REVERT: C 369 ASN cc_start: 0.6685 (m110) cc_final: 0.6423 (m110) REVERT: A 193 MET cc_start: 0.8824 (tpt) cc_final: 0.8520 (tpp) REVERT: A 276 PHE cc_start: 0.7844 (m-10) cc_final: 0.6636 (t80) REVERT: A 369 ASN cc_start: 0.6847 (OUTLIER) cc_final: 0.6233 (p0) REVERT: A 370 LYS cc_start: 0.7830 (ttpt) cc_final: 0.7298 (tttm) REVERT: A 371 GLU cc_start: 0.7703 (mp0) cc_final: 0.7417 (mp0) REVERT: A 372 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7366 (mt-10) REVERT: D 119 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7438 (tp30) REVERT: D 194 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8284 (ttpp) REVERT: D 276 PHE cc_start: 0.7615 (t80) cc_final: 0.7373 (t80) REVERT: D 369 ASN cc_start: 0.6652 (m110) cc_final: 0.6283 (p0) REVERT: D 370 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7768 (ttpp) REVERT: E 51 ARG cc_start: 0.7872 (mmt-90) cc_final: 0.7446 (mmt180) REVERT: E 61 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7314 (mmp) REVERT: E 119 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: E 276 PHE cc_start: 0.7543 (t80) cc_final: 0.7304 (t80) REVERT: E 369 ASN cc_start: 0.6830 (m110) cc_final: 0.6284 (p0) REVERT: E 370 LYS cc_start: 0.7904 (ttpt) cc_final: 0.7332 (ttpp) REVERT: E 373 MET cc_start: 0.8219 (mtp) cc_final: 0.7955 (mtm) outliers start: 27 outliers final: 16 residues processed: 226 average time/residue: 0.6991 time to fit residues: 172.6683 Evaluate side-chains 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 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 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 A residue 369 ASN Chi-restraints excluded: chain D residue 75 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 61 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 36 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.107159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.077063 restraints weight = 19717.882| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.63 r_work: 0.2825 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16735 Z= 0.209 Angle : 0.576 9.011 22560 Z= 0.299 Chirality : 0.043 0.196 2385 Planarity : 0.005 0.038 2770 Dihedral : 11.675 121.567 2644 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.65 % Allowed : 12.21 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.19), residues: 1870 helix: 1.76 (0.15), residues: 1205 sheet: None (None), residues: 0 loop : 0.26 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 51 TYR 0.026 0.002 TYR D 97 PHE 0.025 0.002 PHE A 248 TRP 0.017 0.002 TRP C 309 HIS 0.005 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00489 (16735) covalent geometry : angle 0.57635 (22560) hydrogen bonds : bond 0.06578 ( 975) hydrogen bonds : angle 4.45033 ( 2850) *********************** 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 235 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.612 Fit side-chains REVERT: B 61 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7770 (tpp) REVERT: B 119 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7892 (tp30) REVERT: B 262 LYS cc_start: 0.7360 (mptp) cc_final: 0.6967 (mmmt) REVERT: C 119 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: C 193 MET cc_start: 0.8852 (tpt) cc_final: 0.8529 (tpp) REVERT: C 259 ASN cc_start: 0.7299 (t0) cc_final: 0.6795 (t0) REVERT: C 276 PHE cc_start: 0.7810 (m-80) cc_final: 0.6451 (t80) REVERT: C 355 ARG cc_start: 0.8007 (ttp-170) cc_final: 0.7675 (ttt90) REVERT: A 276 PHE cc_start: 0.7864 (m-10) cc_final: 0.6599 (t80) REVERT: A 369 ASN cc_start: 0.6879 (OUTLIER) cc_final: 0.6260 (p0) REVERT: A 370 LYS cc_start: 0.7873 (ttpt) cc_final: 0.7309 (tttm) REVERT: A 371 GLU cc_start: 0.7633 (mp0) cc_final: 0.7390 (mp0) REVERT: D 57 GLU cc_start: 0.7740 (mp0) cc_final: 0.7281 (pm20) REVERT: D 119 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7456 (tp30) REVERT: D 194 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8281 (ttpp) REVERT: D 276 PHE cc_start: 0.7628 (t80) cc_final: 0.7374 (t80) REVERT: D 369 ASN cc_start: 0.6697 (m110) cc_final: 0.6277 (p0) REVERT: D 370 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7731 (ttpp) REVERT: E 51 ARG cc_start: 0.7817 (mmt-90) cc_final: 0.7394 (mmt180) REVERT: E 61 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7319 (mmp) REVERT: E 119 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: E 276 PHE cc_start: 0.7595 (t80) cc_final: 0.7317 (t80) REVERT: E 370 LYS cc_start: 0.7913 (ttpt) cc_final: 0.7344 (ttpp) outliers start: 28 outliers final: 18 residues processed: 220 average time/residue: 0.7075 time to fit residues: 169.9154 Evaluate side-chains 229 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 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 C residue 205 ILE 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 A residue 369 ASN Chi-restraints excluded: chain D residue 75 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 61 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 97 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.111674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.080974 restraints weight = 20129.605| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.65 r_work: 0.2873 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1677 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= 0.132 Angle : 0.522 10.092 22560 Z= 0.266 Chirality : 0.039 0.264 2385 Planarity : 0.004 0.034 2770 Dihedral : 11.205 120.580 2644 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.19), residues: 1870 helix: 1.75 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.30 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 51 TYR 0.020 0.001 TYR D 97 PHE 0.022 0.001 PHE E 80 TRP 0.014 0.002 TRP C 309 HIS 0.004 0.001 HIS E 178 Details of bonding type rmsd covalent geometry : bond 0.00282 (16735) covalent geometry : angle 0.52173 (22560) hydrogen bonds : bond 0.05700 ( 975) hydrogen bonds : angle 4.33349 ( 2850) ********************** 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 237 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.605 Fit side-chains REVERT: B 61 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7786 (tpp) REVERT: B 119 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: B 262 LYS cc_start: 0.7397 (mptp) cc_final: 0.7005 (mmmt) REVERT: C 119 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: C 193 MET cc_start: 0.8853 (tpt) cc_final: 0.8562 (tpp) REVERT: C 259 ASN cc_start: 0.7280 (t0) cc_final: 0.6787 (t0) REVERT: C 355 ARG cc_start: 0.8060 (ttp-170) cc_final: 0.7627 (ttt90) REVERT: C 369 ASN cc_start: 0.6709 (m110) cc_final: 0.6393 (m110) REVERT: A 193 MET cc_start: 0.8834 (tpt) cc_final: 0.8540 (tpp) REVERT: A 276 PHE cc_start: 0.7846 (m-10) cc_final: 0.6650 (t80) REVERT: A 369 ASN cc_start: 0.6895 (OUTLIER) cc_final: 0.6312 (p0) REVERT: A 370 LYS cc_start: 0.7835 (ttpt) cc_final: 0.7316 (tttm) REVERT: A 372 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7428 (mt-10) REVERT: D 57 GLU cc_start: 0.7759 (mp0) cc_final: 0.7307 (pm20) REVERT: D 119 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7448 (tp30) REVERT: D 194 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8306 (ttpp) REVERT: D 276 PHE cc_start: 0.7636 (t80) cc_final: 0.7397 (t80) REVERT: D 369 ASN cc_start: 0.6660 (m110) cc_final: 0.6243 (p0) REVERT: D 370 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7746 (ttpp) REVERT: E 51 ARG cc_start: 0.7829 (mmt-90) cc_final: 0.7453 (mmt180) REVERT: E 61 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7327 (mmp) REVERT: E 119 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: E 276 PHE cc_start: 0.7537 (t80) cc_final: 0.7276 (t80) REVERT: E 369 ASN cc_start: 0.6830 (m110) cc_final: 0.6296 (p0) REVERT: E 370 LYS cc_start: 0.7918 (ttpt) cc_final: 0.7344 (ttpp) REVERT: E 373 MET cc_start: 0.8202 (mtp) cc_final: 0.7937 (mtm) outliers start: 24 outliers final: 16 residues processed: 225 average time/residue: 0.7150 time to fit residues: 175.3683 Evaluate side-chains 233 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 75 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 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 A residue 369 ASN Chi-restraints excluded: chain D residue 75 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 61 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 184 optimal weight: 0.0470 chunk 32 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.113585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.083102 restraints weight = 20260.821| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.65 r_work: 0.2910 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16735 Z= 0.117 Angle : 0.502 10.566 22560 Z= 0.254 Chirality : 0.038 0.258 2385 Planarity : 0.004 0.032 2770 Dihedral : 10.627 117.389 2644 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.36 % Allowed : 12.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.19), residues: 1870 helix: 1.80 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.30 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 51 TYR 0.016 0.001 TYR D 97 PHE 0.016 0.001 PHE A 80 TRP 0.012 0.001 TRP C 93 HIS 0.003 0.001 HIS E 178 Details of bonding type rmsd covalent geometry : bond 0.00242 (16735) covalent geometry : angle 0.50230 (22560) hydrogen bonds : bond 0.05276 ( 975) hydrogen bonds : angle 4.25420 ( 2850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6845.96 seconds wall clock time: 116 minutes 50.23 seconds (7010.23 seconds total)