Starting phenix.real_space_refine on Fri Jul 3 21:49:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d1l_27134/07_2026/8d1l_27134.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1l_27134/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d1l_27134/07_2026/8d1l_27134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1l_27134/07_2026/8d1l_27134.map" model { file = "/net/cci-nas-00/data/ceres_data/8d1l_27134/07_2026/8d1l_27134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1l_27134/07_2026/8d1l_27134.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d1l_27134/07_2026/8d1l_27134.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d1l_27134/07_2026/8d1l_27134.cif" } 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-6108/lib/python3.11/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: 130 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: 130 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: 130 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: 130 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: 130 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: 3.22, per 1000 atoms: 0.20 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: 1.40 Conformation dependent library (CDL) restraints added in 501.6 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: 0.46 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: 2.09 Time building geometry restraints manager: 1.75 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: 9200 26.43 - 52.87: 545 52.87 - 79.30: 120 79.30 - 105.74: 15 105.74 - 132.17: 5 Dihedral angle restraints: 9885 sinusoidal: 4320 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 9882 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: 5.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.560 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 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 : 17.558 132.174 6295 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/Z covalent geometry : bond 0.00497 / 0.24 (16735) covalent geometry : angle 0.94349 / 0.41 (22560) hydrogen bonds : bond 0.13205 / 8.91 ( 975) hydrogen bonds : angle 5.21751 / 3.73 ( 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 : 0.373 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: 0.5973 time to fit residues: 151.5963 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 : 0.581 ------------------------------------------------------------------------------- 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... ** 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 = 0.111618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.080579 restraints weight = 20163.886| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.66 r_work: 0.2864 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16735 Z= 0.142 Angle : 0.525 8.235 22560 Z= 0.274 Chirality : 0.039 0.150 2385 Planarity : 0.004 0.030 2770 Dihedral : 13.402 124.204 2604 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.83 % Allowed : 10.32 % Favored : 87.85 % 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: 1.76 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.41 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 25 TYR 0.020 0.002 TYR E 97 PHE 0.019 0.001 PHE E 276 TRP 0.013 0.002 TRP E 309 HIS 0.004 0.001 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (16735) covalent geometry : angle 0.52515 / 0.27 (22560) hydrogen bonds : bond 0.05996 / 3.97 ( 975) hydrogen bonds : angle 4.37830 / 3.16 ( 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 : 0.448 Fit side-chains REVERT: B 72 TYR cc_start: 0.6608 (m-80) cc_final: 0.6270 (m-80) REVERT: B 119 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: B 369 ASN cc_start: 0.7163 (m110) cc_final: 0.6190 (p0) REVERT: B 372 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7224 (mt-10) REVERT: C 119 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: C 193 MET cc_start: 0.8875 (tpt) cc_final: 0.8553 (tpp) REVERT: C 276 PHE cc_start: 0.7932 (m-80) cc_final: 0.6431 (t80) REVERT: C 369 ASN cc_start: 0.6724 (m110) cc_final: 0.6118 (p0) REVERT: C 372 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7661 (mt-10) REVERT: A 68 TYR cc_start: 0.5311 (t80) cc_final: 0.4786 (t80) REVERT: A 276 PHE cc_start: 0.7900 (m-10) cc_final: 0.6674 (t80) REVERT: A 369 ASN cc_start: 0.7061 (m110) cc_final: 0.6555 (p0) REVERT: A 370 LYS cc_start: 0.7928 (ttpt) cc_final: 0.7423 (tttt) REVERT: A 372 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7402 (mt-10) REVERT: D 119 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7330 (tp30) REVERT: D 194 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8288 (ttpp) REVERT: D 276 PHE cc_start: 0.7313 (t80) cc_final: 0.7100 (t80) REVERT: D 369 ASN cc_start: 0.6777 (OUTLIER) cc_final: 0.6180 (p0) REVERT: D 370 LYS cc_start: 0.7959 (ttpt) cc_final: 0.7394 (ttpp) REVERT: D 371 GLU cc_start: 0.7610 (mp0) cc_final: 0.7379 (mp0) REVERT: D 372 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7443 (mt-10) REVERT: E 61 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7310 (mmp) REVERT: E 119 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7823 (mp0) REVERT: E 276 PHE cc_start: 0.7483 (t80) cc_final: 0.6800 (m-80) REVERT: E 369 ASN cc_start: 0.6847 (m110) cc_final: 0.6474 (p0) REVERT: E 370 LYS cc_start: 0.7889 (ttpt) cc_final: 0.7364 (ttpp) outliers start: 31 outliers final: 16 residues processed: 224 average time/residue: 0.5750 time to fit residues: 142.0289 Evaluate side-chains 218 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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: 0.5980 chunk 75 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 128 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 73 optimal weight: 0.0010 chunk 172 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3445 r_free = 0.3445 target = 0.113901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.083183 restraints weight = 20275.961| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.66 r_work: 0.2908 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16735 Z= 0.117 Angle : 0.478 7.348 22560 Z= 0.249 Chirality : 0.037 0.148 2385 Planarity : 0.004 0.043 2770 Dihedral : 12.191 116.799 2600 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.24 % Allowed : 10.44 % Favored : 87.32 % 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 : 0.44 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 51 TYR 0.017 0.001 TYR C 68 PHE 0.015 0.001 PHE D 80 TRP 0.011 0.001 TRP B 309 HIS 0.003 0.001 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (16735) covalent geometry : angle 0.47805 / 0.25 (22560) hydrogen bonds : bond 0.05390 / 3.57 ( 975) hydrogen bonds : angle 4.20011 / 3.04 ( 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 255 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 0.598 Fit side-chains REVERT: B 61 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7766 (tpp) REVERT: B 119 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: B 355 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7730 (ttt180) REVERT: B 369 ASN cc_start: 0.7065 (m110) cc_final: 0.6194 (p0) REVERT: B 372 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7249 (mt-10) REVERT: C 61 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6732 (tmt) REVERT: C 119 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: C 169 LYS cc_start: 0.7941 (mttp) cc_final: 0.7599 (mtpp) REVERT: C 193 MET cc_start: 0.8857 (tpt) cc_final: 0.8549 (tpp) REVERT: C 355 ARG cc_start: 0.8058 (ttp-170) cc_final: 0.7767 (ttt90) REVERT: C 369 ASN cc_start: 0.6768 (m110) cc_final: 0.6185 (p0) REVERT: C 372 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7627 (mt-10) REVERT: A 193 MET cc_start: 0.8824 (tpt) cc_final: 0.8527 (tpp) REVERT: A 276 PHE cc_start: 0.7886 (m-10) cc_final: 0.6678 (t80) REVERT: A 369 ASN cc_start: 0.6920 (OUTLIER) cc_final: 0.6352 (p0) REVERT: A 370 LYS cc_start: 0.7987 (ttpt) cc_final: 0.7463 (tttm) REVERT: A 372 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7330 (mt-10) REVERT: D 57 GLU cc_start: 0.7708 (mp0) cc_final: 0.7303 (pm20) REVERT: D 119 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7324 (tp30) REVERT: D 194 LYS cc_start: 0.8529 (ttmt) cc_final: 0.8259 (ttpp) REVERT: D 276 PHE cc_start: 0.7429 (t80) cc_final: 0.7151 (t80) REVERT: D 369 ASN cc_start: 0.6758 (OUTLIER) cc_final: 0.6214 (p0) REVERT: D 370 LYS cc_start: 0.8049 (ttpt) cc_final: 0.7496 (ttpp) REVERT: D 371 GLU cc_start: 0.7595 (mp0) cc_final: 0.7300 (mp0) REVERT: D 372 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7352 (mt-10) REVERT: E 25 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7865 (mtp-110) REVERT: E 61 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7306 (mmp) REVERT: E 119 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7397 (tp30) REVERT: E 163 MET cc_start: 0.8938 (ttp) cc_final: 0.8738 (ttm) REVERT: E 276 PHE cc_start: 0.7606 (t80) cc_final: 0.6846 (m-80) REVERT: E 369 ASN cc_start: 0.6757 (m110) cc_final: 0.6242 (p0) REVERT: E 370 LYS cc_start: 0.7925 (ttpt) cc_final: 0.7360 (ttpp) REVERT: E 372 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7616 (mt-10) REVERT: E 373 MET cc_start: 0.8227 (mtp) cc_final: 0.7969 (mtm) outliers start: 38 outliers final: 15 residues processed: 239 average time/residue: 0.5944 time to fit residues: 156.5684 Evaluate side-chains 232 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 61 MET 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 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 249 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 17 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 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: 5.9990 chunk 141 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3371 r_free = 0.3371 target = 0.108513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.077224 restraints weight = 20336.179| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.67 r_work: 0.2808 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16735 Z= 0.239 Angle : 0.589 8.031 22560 Z= 0.309 Chirality : 0.044 0.160 2385 Planarity : 0.005 0.041 2770 Dihedral : 12.194 114.595 2600 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.54 % Allowed : 9.97 % 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: 1.61 (0.19), residues: 1870 helix: 1.60 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : 0.14 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 51 TYR 0.027 0.002 TYR E 97 PHE 0.028 0.002 PHE A 248 TRP 0.018 0.002 TRP C 309 HIS 0.007 0.002 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.24 (16735) covalent geometry : angle 0.58899 / 0.31 (22560) hydrogen bonds : bond 0.06923 / 4.59 ( 975) hydrogen bonds : angle 4.48058 / 3.23 ( 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 248 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 0.629 Fit side-chains REVERT: B 119 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7943 (tp30) REVERT: B 374 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: C 61 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6831 (tmt) REVERT: C 119 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: C 193 MET cc_start: 0.8851 (tpt) cc_final: 0.8521 (tpp) REVERT: A 68 TYR cc_start: 0.5379 (t80) cc_final: 0.4897 (t80) REVERT: A 276 PHE cc_start: 0.7941 (m-10) cc_final: 0.6650 (t80) REVERT: A 369 ASN cc_start: 0.7021 (OUTLIER) cc_final: 0.6359 (p0) REVERT: A 370 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7437 (tttm) REVERT: A 371 GLU cc_start: 0.7548 (mp0) cc_final: 0.7317 (mp0) REVERT: A 372 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7454 (mt-10) REVERT: D 57 GLU cc_start: 0.7703 (mp0) cc_final: 0.7282 (pm20) REVERT: D 119 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7436 (tp30) REVERT: D 194 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8316 (ttpp) REVERT: D 262 LYS cc_start: 0.7578 (mmmm) cc_final: 0.7326 (mmmt) REVERT: D 276 PHE cc_start: 0.7519 (t80) cc_final: 0.7226 (t80) REVERT: D 355 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7409 (ttt180) REVERT: D 369 ASN cc_start: 0.6748 (m110) cc_final: 0.6248 (p0) REVERT: D 370 LYS cc_start: 0.8017 (ttpt) cc_final: 0.7513 (ttpp) REVERT: D 372 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7453 (mt-10) REVERT: E 61 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7327 (mmp) REVERT: E 119 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7514 (tp30) REVERT: E 276 PHE cc_start: 0.7631 (t80) cc_final: 0.6832 (m-80) REVERT: E 370 LYS cc_start: 0.7902 (ttpt) cc_final: 0.7337 (ttpp) outliers start: 43 outliers final: 20 residues processed: 231 average time/residue: 0.6087 time to fit residues: 154.7762 Evaluate side-chains 232 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 374 GLU Chi-restraints excluded: chain C residue 61 MET 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: 4.9990 chunk 50 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.080868 restraints weight = 20260.558| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.67 r_work: 0.2870 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16735 Z= 0.138 Angle : 0.505 7.336 22560 Z= 0.263 Chirality : 0.038 0.149 2385 Planarity : 0.004 0.036 2770 Dihedral : 11.521 109.659 2598 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.83 % Allowed : 11.39 % 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: 1.87 (0.19), residues: 1870 helix: 1.77 (0.15), 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 E 25 TYR 0.020 0.001 TYR E 97 PHE 0.017 0.001 PHE C 248 TRP 0.014 0.002 TRP C 309 HIS 0.004 0.001 HIS E 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (16735) covalent geometry : angle 0.50529 / 0.26 (22560) hydrogen bonds : bond 0.05757 / 3.81 ( 975) hydrogen bonds : angle 4.29634 / 3.10 ( 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 239 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.596 Fit side-chains REVERT: B 72 TYR cc_start: 0.6415 (m-80) cc_final: 0.6204 (m-80) REVERT: B 119 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7883 (tp30) REVERT: B 370 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7937 (ttpt) REVERT: C 119 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: C 193 MET cc_start: 0.8863 (tpt) cc_final: 0.8568 (tpp) REVERT: C 355 ARG cc_start: 0.8056 (ttp-170) cc_final: 0.7629 (ttt90) REVERT: A 193 MET cc_start: 0.8821 (tpt) cc_final: 0.8530 (tpp) REVERT: A 276 PHE cc_start: 0.7841 (m-10) cc_final: 0.6636 (t80) REVERT: A 369 ASN cc_start: 0.6913 (OUTLIER) cc_final: 0.6184 (p0) REVERT: A 370 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7376 (tttm) REVERT: A 371 GLU cc_start: 0.7609 (mp0) cc_final: 0.7295 (mp0) REVERT: A 372 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7322 (mt-10) REVERT: D 57 GLU cc_start: 0.7744 (mp0) cc_final: 0.7311 (pm20) REVERT: D 119 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: D 194 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8279 (ttpp) REVERT: D 276 PHE cc_start: 0.7519 (t80) cc_final: 0.7243 (t80) REVERT: D 369 ASN cc_start: 0.6690 (OUTLIER) cc_final: 0.6144 (p0) REVERT: D 370 LYS cc_start: 0.8050 (ttpt) cc_final: 0.7450 (ttpp) REVERT: D 372 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7356 (mt-10) REVERT: E 25 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7855 (mtp-110) REVERT: E 51 ARG cc_start: 0.7954 (mmt-90) cc_final: 0.7436 (mpt90) REVERT: E 61 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7292 (mmp) REVERT: E 119 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7474 (tp30) REVERT: E 276 PHE cc_start: 0.7552 (t80) cc_final: 0.7279 (t80) REVERT: E 369 ASN cc_start: 0.6852 (m110) cc_final: 0.6328 (p0) REVERT: E 370 LYS cc_start: 0.7925 (ttpt) cc_final: 0.7377 (ttpp) outliers start: 31 outliers final: 17 residues processed: 225 average time/residue: 0.6101 time to fit residues: 150.8106 Evaluate side-chains 227 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 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: 0.8980 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: 0.5980 chunk 149 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3403 r_free = 0.3403 target = 0.110769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.079823 restraints weight = 20249.170| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.66 r_work: 0.2853 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1480 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= 0.155 Angle : 0.521 7.345 22560 Z= 0.271 Chirality : 0.039 0.150 2385 Planarity : 0.004 0.035 2770 Dihedral : 11.264 105.817 2596 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.83 % Allowed : 11.74 % Favored : 86.43 % 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 (0.15), residues: 1215 sheet: None (None), residues: 0 loop : 0.40 (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 0.019 0.001 PHE C 248 TRP 0.015 0.002 TRP A 309 HIS 0.004 0.001 HIS E 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (16735) covalent geometry : angle 0.52072 / 0.27 (22560) hydrogen bonds : bond 0.05982 / 3.97 ( 975) hydrogen bonds : angle 4.31818 / 3.12 ( 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 235 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: B 119 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7874 (tp30) REVERT: B 262 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7082 (mmmt) REVERT: C 119 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: C 193 MET cc_start: 0.8860 (tpt) cc_final: 0.8561 (tpp) REVERT: C 276 PHE cc_start: 0.7859 (m-80) cc_final: 0.6512 (t80) REVERT: C 355 ARG cc_start: 0.8043 (ttp-170) cc_final: 0.7745 (ttt90) REVERT: A 193 MET cc_start: 0.8825 (tpt) cc_final: 0.8526 (tpp) REVERT: A 276 PHE cc_start: 0.7857 (m-10) cc_final: 0.6637 (t80) REVERT: A 369 ASN cc_start: 0.6824 (OUTLIER) cc_final: 0.6260 (p0) REVERT: A 370 LYS cc_start: 0.7844 (ttpt) cc_final: 0.7286 (tttm) REVERT: A 371 GLU cc_start: 0.7739 (mp0) cc_final: 0.7497 (mp0) REVERT: D 57 GLU cc_start: 0.7752 (mp0) cc_final: 0.7367 (pm20) REVERT: D 119 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7422 (tp30) REVERT: D 194 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8276 (ttpp) REVERT: D 276 PHE cc_start: 0.7595 (t80) cc_final: 0.7326 (t80) REVERT: D 355 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7405 (ttt180) REVERT: D 369 ASN cc_start: 0.6672 (m110) cc_final: 0.6207 (p0) REVERT: D 370 LYS cc_start: 0.8080 (ttpt) cc_final: 0.7605 (ttpp) REVERT: D 371 GLU cc_start: 0.7516 (mp0) cc_final: 0.7221 (mp0) REVERT: D 372 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7421 (mt-10) REVERT: E 25 ARG cc_start: 0.8068 (mtp85) cc_final: 0.7856 (mtp-110) REVERT: E 61 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7334 (mmp) REVERT: E 119 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7436 (tp30) REVERT: E 276 PHE cc_start: 0.7538 (t80) cc_final: 0.7303 (t80) REVERT: E 369 ASN cc_start: 0.6840 (m110) cc_final: 0.6325 (p0) REVERT: E 370 LYS cc_start: 0.7937 (ttpt) cc_final: 0.7387 (ttpp) outliers start: 31 outliers final: 18 residues processed: 223 average time/residue: 0.6112 time to fit residues: 149.6683 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 : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 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 249 LEU Chi-restraints excluded: chain E residue 374 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 141 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 111 optimal weight: 0.0070 chunk 156 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3409 r_free = 0.3409 target = 0.111180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.080317 restraints weight = 20132.050| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.66 r_work: 0.2861 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1542 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= 0.148 Angle : 0.518 7.327 22560 Z= 0.268 Chirality : 0.039 0.150 2385 Planarity : 0.004 0.035 2770 Dihedral : 11.030 103.055 2594 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.95 % Allowed : 11.74 % 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: 1.88 (0.19), residues: 1870 helix: 1.80 (0.15), residues: 1210 sheet: None (None), residues: 0 loop : 0.34 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 51 TYR 0.021 0.002 TYR D 97 PHE 0.018 0.001 PHE C 248 TRP 0.014 0.002 TRP A 309 HIS 0.004 0.001 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (16735) covalent geometry : angle 0.51769 / 0.27 (22560) hydrogen bonds : bond 0.05867 / 3.89 ( 975) hydrogen bonds : angle 4.30399 / 3.11 ( 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 242 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: B 119 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: C 119 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: C 193 MET cc_start: 0.8860 (tpt) cc_final: 0.8562 (tpp) REVERT: C 276 PHE cc_start: 0.7781 (m-80) cc_final: 0.6507 (t80) REVERT: C 355 ARG cc_start: 0.8045 (ttp-170) cc_final: 0.7750 (ttt90) REVERT: A 193 MET cc_start: 0.8819 (tpt) cc_final: 0.8521 (tpp) REVERT: A 276 PHE cc_start: 0.7849 (m-10) cc_final: 0.6638 (t80) REVERT: A 369 ASN cc_start: 0.6952 (OUTLIER) cc_final: 0.6386 (p0) REVERT: A 370 LYS cc_start: 0.7836 (ttpt) cc_final: 0.7303 (tttm) REVERT: D 57 GLU cc_start: 0.7776 (mp0) cc_final: 0.7372 (pm20) REVERT: D 119 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7437 (tp30) REVERT: D 194 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8263 (ttpp) REVERT: D 276 PHE cc_start: 0.7580 (t80) cc_final: 0.7342 (t80) REVERT: D 355 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7400 (ttt180) REVERT: D 369 ASN cc_start: 0.6685 (m110) cc_final: 0.6212 (p0) REVERT: D 370 LYS cc_start: 0.8088 (ttpt) cc_final: 0.7607 (ttpp) REVERT: D 371 GLU cc_start: 0.7512 (mp0) cc_final: 0.7193 (mp0) REVERT: E 25 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7849 (mtp-110) REVERT: E 61 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7307 (mmp) REVERT: E 119 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7476 (tp30) REVERT: E 276 PHE cc_start: 0.7532 (t80) cc_final: 0.7307 (t80) REVERT: E 369 ASN cc_start: 0.6830 (m110) cc_final: 0.6325 (p0) REVERT: E 370 LYS cc_start: 0.7935 (ttpt) cc_final: 0.7386 (ttpp) outliers start: 33 outliers final: 18 residues processed: 228 average time/residue: 0.6015 time to fit residues: 150.7104 Evaluate side-chains 233 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain 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 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 Chi-restraints excluded: chain E residue 374 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 180 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3397 r_free = 0.3397 target = 0.110259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.079204 restraints weight = 20336.003| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.66 r_work: 0.2843 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16735 Z= 0.169 Angle : 0.540 7.508 22560 Z= 0.280 Chirality : 0.040 0.153 2385 Planarity : 0.004 0.036 2770 Dihedral : 11.053 101.386 2594 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.77 % Allowed : 12.09 % 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: 1.85 (0.19), residues: 1870 helix: 1.75 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : 0.36 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 51 TYR 0.023 0.002 TYR D 97 PHE 0.021 0.002 PHE C 248 TRP 0.015 0.002 TRP A 309 HIS 0.006 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (16735) covalent geometry : angle 0.54004 / 0.28 (22560) hydrogen bonds : bond 0.06155 / 4.08 ( 975) hydrogen bonds : angle 4.36590 / 3.15 ( 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 238 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.545 Fit side-chains REVERT: B 119 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7877 (tp30) REVERT: B 262 LYS cc_start: 0.7368 (mptp) cc_final: 0.7139 (mmmt) REVERT: C 51 ARG cc_start: 0.7847 (mtt-85) cc_final: 0.7470 (mpt-90) REVERT: C 119 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: C 193 MET cc_start: 0.8857 (tpt) cc_final: 0.8552 (tpp) REVERT: C 276 PHE cc_start: 0.7767 (m-80) cc_final: 0.6495 (t80) REVERT: C 355 ARG cc_start: 0.8004 (ttp-170) cc_final: 0.7689 (ttt90) REVERT: C 369 ASN cc_start: 0.6741 (m110) cc_final: 0.6444 (m110) REVERT: A 193 MET cc_start: 0.8819 (tpt) cc_final: 0.8514 (tpp) REVERT: A 276 PHE cc_start: 0.7870 (m-10) cc_final: 0.6638 (t80) REVERT: A 369 ASN cc_start: 0.6947 (OUTLIER) cc_final: 0.6420 (p0) REVERT: A 370 LYS cc_start: 0.7817 (ttpt) cc_final: 0.7283 (tttm) REVERT: D 57 GLU cc_start: 0.7758 (mp0) cc_final: 0.7362 (pm20) REVERT: D 119 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7436 (tp30) REVERT: D 194 LYS cc_start: 0.8549 (ttmt) cc_final: 0.8279 (ttpp) REVERT: D 276 PHE cc_start: 0.7593 (t80) cc_final: 0.7358 (t80) REVERT: D 355 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7395 (ttt180) REVERT: D 370 LYS cc_start: 0.8073 (ttpt) cc_final: 0.7556 (ttpp) REVERT: E 25 ARG cc_start: 0.8045 (mtp85) cc_final: 0.7822 (mtp-110) REVERT: E 51 ARG cc_start: 0.7975 (mmt-90) cc_final: 0.7511 (mpt90) REVERT: E 61 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7313 (mmp) REVERT: E 119 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7480 (tp30) REVERT: E 276 PHE cc_start: 0.7551 (t80) cc_final: 0.7244 (t80) REVERT: E 369 ASN cc_start: 0.6848 (m110) cc_final: 0.6270 (p0) REVERT: E 370 LYS cc_start: 0.7908 (ttpt) cc_final: 0.7349 (ttpp) outliers start: 30 outliers final: 19 residues processed: 225 average time/residue: 0.6053 time to fit residues: 149.3099 Evaluate side-chains 229 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain 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 Chi-restraints excluded: chain E residue 374 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 36 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 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: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3396 r_free = 0.3396 target = 0.108311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.078174 restraints weight = 19672.616| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.64 r_work: 0.2844 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1546 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= 0.175 Angle : 0.550 9.141 22560 Z= 0.284 Chirality : 0.041 0.204 2385 Planarity : 0.004 0.036 2770 Dihedral : 11.015 100.588 2594 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.71 % Allowed : 12.21 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.72 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : 0.34 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 51 TYR 0.023 0.002 TYR D 97 PHE 0.021 0.002 PHE C 248 TRP 0.015 0.002 TRP A 309 HIS 0.005 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (16735) covalent geometry : angle 0.55010 / 0.28 (22560) hydrogen bonds : bond 0.06198 / 4.11 ( 975) hydrogen bonds : angle 4.38947 / 3.17 ( 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 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.611 Fit side-chains REVERT: B 119 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7889 (tp30) REVERT: B 262 LYS cc_start: 0.7377 (mptp) cc_final: 0.7150 (mmmt) REVERT: C 119 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: C 193 MET cc_start: 0.8861 (tpt) cc_final: 0.8554 (tpp) REVERT: C 276 PHE cc_start: 0.7772 (m-80) cc_final: 0.6499 (t80) REVERT: C 355 ARG cc_start: 0.8013 (ttp-170) cc_final: 0.7693 (ttt90) REVERT: C 369 ASN cc_start: 0.6696 (m110) cc_final: 0.6446 (m110) REVERT: A 193 MET cc_start: 0.8824 (tpt) cc_final: 0.8520 (tpp) REVERT: A 276 PHE cc_start: 0.7884 (m-10) cc_final: 0.6657 (t80) REVERT: A 369 ASN cc_start: 0.6945 (OUTLIER) cc_final: 0.6494 (p0) REVERT: A 370 LYS cc_start: 0.7801 (ttpt) cc_final: 0.7273 (tttm) REVERT: D 57 GLU cc_start: 0.7759 (mp0) cc_final: 0.7361 (pm20) REVERT: D 119 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7438 (tp30) REVERT: D 194 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8293 (ttpp) REVERT: D 276 PHE cc_start: 0.7621 (t80) cc_final: 0.7375 (t80) REVERT: D 355 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7417 (ttt180) REVERT: D 370 LYS cc_start: 0.8047 (ttpt) cc_final: 0.7550 (ttpp) REVERT: E 25 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7824 (mtp-110) REVERT: E 51 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.7528 (mpt90) REVERT: E 61 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7323 (mmp) REVERT: E 119 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7480 (tp30) REVERT: E 276 PHE cc_start: 0.7605 (t80) cc_final: 0.7327 (t80) REVERT: E 369 ASN cc_start: 0.6919 (m110) cc_final: 0.6299 (p0) REVERT: E 370 LYS cc_start: 0.7923 (ttpt) cc_final: 0.7366 (ttpp) outliers start: 29 outliers final: 20 residues processed: 219 average time/residue: 0.5962 time to fit residues: 143.3732 Evaluate side-chains 228 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 114 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 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 = 0.3418 r_free = 0.3418 target = 0.111821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.081019 restraints weight = 20091.844| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.66 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: 0.8662 moved from start: 0.1652 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= 0.135 Angle : 0.526 10.280 22560 Z= 0.267 Chirality : 0.040 0.261 2385 Planarity : 0.004 0.034 2770 Dihedral : 10.688 98.177 2594 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.42 % Allowed : 12.63 % Favored : 85.96 % 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: 1.83 (0.19), residues: 1870 helix: 1.77 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.30 (0.23), 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 0.019 0.001 PHE E 80 TRP 0.014 0.002 TRP B 309 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (16735) covalent geometry : angle 0.52552 / 0.27 (22560) hydrogen bonds : bond 0.05698 / 3.78 ( 975) hydrogen bonds : angle 4.32843 / 3.13 ( 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 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: B 119 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7910 (tp30) REVERT: B 262 LYS cc_start: 0.7400 (mptp) cc_final: 0.7024 (mmmt) REVERT: C 51 ARG cc_start: 0.7876 (mtt-85) cc_final: 0.7471 (mpt-90) REVERT: C 119 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: C 193 MET cc_start: 0.8861 (tpt) cc_final: 0.8564 (tpp) REVERT: C 276 PHE cc_start: 0.7712 (m-80) cc_final: 0.6489 (t80) REVERT: C 355 ARG cc_start: 0.8051 (ttp-170) cc_final: 0.7617 (ttt90) REVERT: C 369 ASN cc_start: 0.6681 (m110) cc_final: 0.6473 (m110) REVERT: A 193 MET cc_start: 0.8823 (tpt) cc_final: 0.8526 (tpp) REVERT: A 276 PHE cc_start: 0.7900 (m-10) cc_final: 0.6669 (t80) REVERT: A 369 ASN cc_start: 0.6960 (m110) cc_final: 0.6497 (p0) REVERT: A 370 LYS cc_start: 0.7817 (ttpt) cc_final: 0.7291 (tttm) REVERT: D 57 GLU cc_start: 0.7707 (mp0) cc_final: 0.7339 (pm20) REVERT: D 119 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7425 (tp30) REVERT: D 194 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8315 (ttpp) REVERT: D 276 PHE cc_start: 0.7617 (t80) cc_final: 0.7386 (t80) REVERT: D 355 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7402 (ttt180) REVERT: D 370 LYS cc_start: 0.8061 (ttpt) cc_final: 0.7555 (ttpp) REVERT: D 371 GLU cc_start: 0.7515 (mp0) cc_final: 0.7201 (mp0) REVERT: E 25 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7847 (mtp-110) REVERT: E 61 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7332 (mmp) REVERT: E 119 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7465 (tp30) REVERT: E 276 PHE cc_start: 0.7555 (t80) cc_final: 0.7288 (t80) REVERT: E 369 ASN cc_start: 0.6846 (m110) cc_final: 0.6282 (p0) REVERT: E 370 LYS cc_start: 0.7917 (ttpt) cc_final: 0.7351 (ttpp) outliers start: 24 outliers final: 19 residues processed: 220 average time/residue: 0.6898 time to fit residues: 166.0316 Evaluate side-chains 232 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 203 ASP Chi-restraints excluded: chain A residue 249 LEU 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 67 LEU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3427 r_free = 0.3427 target = 0.112393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.081590 restraints weight = 20195.551| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.66 r_work: 0.2884 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16735 Z= 0.131 Angle : 0.520 10.763 22560 Z= 0.264 Chirality : 0.039 0.249 2385 Planarity : 0.004 0.034 2770 Dihedral : 10.337 95.318 2594 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.59 % Allowed : 12.57 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.19), residues: 1870 helix: 1.79 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.28 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 51 TYR 0.019 0.001 TYR D 97 PHE 0.016 0.001 PHE C 276 TRP 0.013 0.001 TRP B 309 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (16735) covalent geometry : angle 0.51970 / 0.26 (22560) hydrogen bonds : bond 0.05581 / 3.70 ( 975) hydrogen bonds : angle 4.29626 / 3.10 ( 2850) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6097.12 seconds wall clock time: 104 minutes 23.79 seconds (6263.79 seconds total)