Starting phenix.real_space_refine on Sat Jun 14 18:52:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d1l_27134/06_2025/8d1l_27134.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1l_27134/06_2025/8d1l_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_27134/06_2025/8d1l_27134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1l_27134/06_2025/8d1l_27134.map" model { file = "/net/cci-nas-00/data/ceres_data/8d1l_27134/06_2025/8d1l_27134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1l_27134/06_2025/8d1l_27134.cif" } resolution = 2.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 P 5 5.49 5 S 80 5.16 5 Cl 1 4.86 5 C 10905 2.51 5 N 2550 2.21 5 O 2760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16306 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "A" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "B" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {' CA': 1, 'MC3': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 144 Unusual residues: {' CA': 1, ' CL': 1, 'MC3': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 41 Restraints were copied for chains: E, C, D Time building chain proxies: 11.35, per 1000 atoms: 0.70 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=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 23 " distance=0.00 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 42 " distance=0.00 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 69 " distance=0.00 Simple disulfide: pdb=" SG CYS C 221 " - pdb=" SG CYS C 221 " distance=0.00 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 251 " distance=0.00 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: 3.81 Conformation dependent library (CDL) restraints added in 1.8 seconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 5 sheets defined 71.5% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'B' and resid 6 through 10 removed outlier: 3.637A pdb=" N ALA B 10 " --> pdb=" O SER B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 20 removed outlier: 4.004A pdb=" N LEU B 20 " --> pdb=" O SER B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.616A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 72 Processing helix chain 'B' and resid 75 through 99 Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 118 through 144 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.681A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.979A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.751A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.638A pdb=" N ALA C 10 " --> pdb=" O SER C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 20 removed outlier: 4.004A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 27 through 53 removed outlier: 5.616A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 72 Processing helix chain 'C' and resid 75 through 99 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.681A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.979A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.751A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.637A pdb=" N ALA A 10 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 20 removed outlier: 4.004A pdb=" N LEU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.616A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 Processing helix chain 'A' and resid 75 through 99 Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 118 through 144 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.681A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.979A pdb=" N VAL A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.751A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'D' and resid 6 through 10 removed outlier: 3.637A pdb=" N ALA D 10 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 20 removed outlier: 4.004A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.616A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 72 Processing helix chain 'D' and resid 75 through 99 Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 118 through 144 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.680A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.978A pdb=" N VAL D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.751A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 324 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'E' and resid 6 through 10 removed outlier: 3.637A pdb=" N ALA E 10 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 20 removed outlier: 4.004A pdb=" N LEU E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 27 through 53 removed outlier: 5.616A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 72 Processing helix chain 'E' and resid 75 through 99 Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.681A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.979A pdb=" N VAL E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.750A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 Processing helix chain 'E' and resid 351 through 355 Processing sheet with id=AA1, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.494A pdb=" N TYR B 347 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 375 through 376 removed outlier: 4.487A pdb=" N TYR C 347 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 375 through 376 removed outlier: 4.489A pdb=" N TYR D 347 " --> pdb=" O GLN C 376 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 348 removed outlier: 4.479A pdb=" N TYR A 347 " --> pdb=" O GLN E 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 375 through 376 removed outlier: 4.484A pdb=" N TYR E 347 " --> pdb=" O GLN D 376 " (cutoff:3.500A) 975 hydrogen bonds defined for protein. 2850 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.20 Time building geometry restraints manager: 4.51 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: 9230 26.43 - 52.87: 575 52.87 - 79.30: 120 79.30 - 105.74: 15 105.74 - 132.17: 5 Dihedral angle restraints: 9945 sinusoidal: 4380 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 9942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1612 0.034 - 0.067: 566 0.067 - 0.101: 120 0.101 - 0.134: 73 0.134 - 0.168: 14 Chirality restraints: 2385 Sorted by residual: chirality pdb=" CA LEU D 138 " pdb=" N LEU D 138 " pdb=" C LEU D 138 " pdb=" CB LEU D 138 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA LEU B 138 " pdb=" N LEU B 138 " pdb=" C LEU B 138 " pdb=" CB LEU B 138 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA LEU A 138 " pdb=" N LEU A 138 " pdb=" C LEU A 138 " pdb=" CB LEU A 138 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 2382 not shown) Planarity restraints: 2770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 276 " -0.007 2.00e-02 2.50e+03 1.13e-02 2.24e+00 pdb=" CG PHE A 276 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 276 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 276 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 276 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 276 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 276 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 276 " 0.007 2.00e-02 2.50e+03 1.12e-02 2.20e+00 pdb=" CG PHE D 276 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE D 276 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE D 276 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 276 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 276 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 276 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 276 " -0.007 2.00e-02 2.50e+03 1.12e-02 2.19e+00 pdb=" CG PHE E 276 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE E 276 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE E 276 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE E 276 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 276 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 276 " -0.000 2.00e-02 2.50e+03 ... (remaining 2767 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2755 2.76 - 3.29: 15746 3.29 - 3.83: 29403 3.83 - 4.36: 36232 4.36 - 4.90: 59185 Nonbonded interactions: 143321 Sorted by model distance: nonbonded pdb=" NH2 ARG E 51 " pdb=" OD2 ASP E 270 " model vdw 2.222 3.120 nonbonded pdb=" NH2 ARG A 51 " pdb=" OD2 ASP A 270 " model vdw 2.222 3.120 nonbonded pdb=" NH2 ARG C 51 " pdb=" OD2 ASP C 270 " model vdw 2.222 3.120 nonbonded pdb=" NH2 ARG B 51 " pdb=" OD2 ASP B 270 " model vdw 2.222 3.120 nonbonded pdb=" NH2 ARG D 51 " pdb=" OD2 ASP D 270 " model vdw 2.223 3.120 ... (remaining 143316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 377 or resid 603 or (resid 604 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42)) or (resid 605 through 606 and \ (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C \ 39 or name C40 or name C41 or name C42 or name C43 or name C44)) or (resid 607 t \ hrough 608 and (name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C42)) or resid 609)) selection = (chain 'B' and (resid 2 through 377 or (resid 603 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 604 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42)) or (resid 605 through 606 and (name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42 or name C43 or name C44)) or (resid 607 through 608 and \ (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C40 or name C41 or name C42)) or (resid 609 and (name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'C' and (resid 2 through 377 or (resid 603 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 604 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42)) or (resid 605 through 606 and (name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42 or name C43 or name C44)) or (resid 607 through 608 and \ (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C40 or name C41 or name C42)) or (resid 609 and (name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'D' and (resid 2 through 377 or (resid 603 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 604 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40 or name C41 or name C42)) or (resid 605 through 606 and (name C33 or n \ ame C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42 or name C43 or name C44)) or (resid 607 through 608 and \ (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C3 \ 9 or name C40 or name C41 or name C42)) or (resid 609 and (name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name \ C39 or name C40 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'E' and (resid 2 through 377 or resid 603 or (resid 604 and (name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C40 or name C41 or name C42)) or (resid 605 through 606 and \ (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C \ 39 or name C40 or name C41 or name C42 or name C43 or name C44)) or (resid 607 t \ hrough 608 and (name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name C42)) or resid 609)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 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: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.140 Find NCS groups from input model: 1.000 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:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16735 Z= 0.241 Angle : 0.943 22.051 22565 Z= 0.406 Chirality : 0.040 0.168 2385 Planarity : 0.004 0.024 2770 Dihedral : 17.688 132.174 6345 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.18 % Allowed : 9.14 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.19), residues: 1870 helix: 1.54 (0.15), residues: 1235 sheet: None (None), residues: 0 loop : 0.59 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 309 HIS 0.005 0.002 HIS E 178 PHE 0.025 0.002 PHE A 276 TYR 0.022 0.001 TYR C 97 ARG 0.003 0.000 ARG A 130 Details of bonding type rmsd hydrogen bonds : bond 0.13205 ( 975) hydrogen bonds : angle 5.21751 ( 2850) SS BOND : angle 0.00000 ( 5) covalent geometry : bond 0.00497 (16735) covalent geometry : angle 0.94349 (22560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 1.977 Fit side-chains REVERT: C 193 MET cc_start: 0.9014 (tpt) cc_final: 0.8762 (tpp) REVERT: A 68 TYR cc_start: 0.6613 (t80) cc_final: 0.6399 (t80) REVERT: A 193 MET cc_start: 0.8984 (tpt) cc_final: 0.8757 (tpp) REVERT: A 370 LYS cc_start: 0.8620 (ttpt) cc_final: 0.8368 (tttm) REVERT: D 276 PHE cc_start: 0.7633 (t80) cc_final: 0.7334 (m-80) REVERT: D 370 LYS cc_start: 0.8637 (ttpt) cc_final: 0.8148 (ttpp) REVERT: E 276 PHE cc_start: 0.7694 (t80) cc_final: 0.7459 (m-80) REVERT: E 370 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8400 (ttpp) outliers start: 20 outliers final: 7 residues processed: 231 average time/residue: 1.4177 time to fit residues: 360.5840 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 : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain E residue 178 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 0.0970 chunk 145 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.113260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.082394 restraints weight = 20130.135| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.66 r_work: 0.2895 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16735 Z= 0.125 Angle : 0.507 8.102 22565 Z= 0.264 Chirality : 0.038 0.150 2385 Planarity : 0.004 0.029 2770 Dihedral : 13.619 127.246 2654 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.65 % Allowed : 10.32 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.19), residues: 1870 helix: 1.77 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.39 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 309 HIS 0.004 0.001 HIS E 178 PHE 0.017 0.001 PHE E 276 TYR 0.018 0.002 TYR B 68 ARG 0.005 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.05620 ( 975) hydrogen bonds : angle 4.31750 ( 2850) SS BOND : angle 0.00000 ( 5) covalent geometry : bond 0.00261 (16735) covalent geometry : angle 0.50695 (22560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 2.146 Fit side-chains REVERT: B 72 TYR cc_start: 0.6574 (m-80) cc_final: 0.6247 (m-80) REVERT: B 119 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: B 369 ASN cc_start: 0.7172 (m110) cc_final: 0.6281 (p0) REVERT: B 372 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7300 (mt-10) REVERT: C 119 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: C 169 LYS cc_start: 0.7929 (mttp) cc_final: 0.7616 (mtpp) REVERT: C 193 MET cc_start: 0.8864 (tpt) cc_final: 0.8547 (tpp) REVERT: C 276 PHE cc_start: 0.7922 (m-80) cc_final: 0.6434 (t80) REVERT: C 369 ASN cc_start: 0.6714 (m110) cc_final: 0.6208 (p0) REVERT: C 372 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7717 (mt-10) REVERT: A 68 TYR cc_start: 0.5236 (t80) cc_final: 0.4673 (t80) REVERT: A 193 MET cc_start: 0.8820 (tpt) cc_final: 0.8468 (tpp) REVERT: A 276 PHE cc_start: 0.7938 (m-10) cc_final: 0.6697 (t80) REVERT: A 369 ASN cc_start: 0.7018 (OUTLIER) cc_final: 0.6499 (p0) REVERT: A 370 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7406 (tttm) REVERT: A 372 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7392 (mt-10) REVERT: D 119 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7347 (tp30) REVERT: D 194 LYS cc_start: 0.8529 (ttmt) cc_final: 0.8293 (ttpp) REVERT: D 276 PHE cc_start: 0.7315 (t80) cc_final: 0.7102 (t80) REVERT: D 369 ASN cc_start: 0.6813 (OUTLIER) cc_final: 0.6227 (p0) REVERT: D 370 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7359 (ttpp) REVERT: D 372 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7394 (mt-10) REVERT: E 61 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7325 (mmp) REVERT: E 119 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: E 276 PHE cc_start: 0.7498 (t80) cc_final: 0.6781 (m-80) REVERT: E 369 ASN cc_start: 0.6857 (m110) cc_final: 0.6501 (p0) REVERT: E 370 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7255 (ttpp) outliers start: 28 outliers final: 15 residues processed: 221 average time/residue: 1.6882 time to fit residues: 412.0529 Evaluate side-chains 212 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain 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 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 114 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.109501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.078323 restraints weight = 20110.147| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.66 r_work: 0.2826 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16735 Z= 0.194 Angle : 0.556 7.711 22565 Z= 0.292 Chirality : 0.042 0.155 2385 Planarity : 0.004 0.035 2770 Dihedral : 12.933 123.453 2650 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.54 % Allowed : 10.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.19), residues: 1870 helix: 1.75 (0.15), residues: 1210 sheet: None (None), residues: 0 loop : 0.38 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 309 HIS 0.006 0.001 HIS D 326 PHE 0.023 0.002 PHE B 248 TYR 0.025 0.002 TYR E 97 ARG 0.005 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.06532 ( 975) hydrogen bonds : angle 4.39811 ( 2850) SS BOND : angle 0.00000 ( 5) covalent geometry : bond 0.00450 (16735) covalent geometry : angle 0.55572 (22560) *********************** 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 239 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 2.239 Fit side-chains REVERT: B 119 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7921 (tp30) REVERT: C 119 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: C 193 MET cc_start: 0.8851 (tpt) cc_final: 0.8535 (tpp) REVERT: C 276 PHE cc_start: 0.7929 (m-80) cc_final: 0.6403 (t80) REVERT: C 369 ASN cc_start: 0.6874 (m110) cc_final: 0.6164 (p0) REVERT: C 372 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 68 TYR cc_start: 0.5240 (t80) cc_final: 0.4686 (t80) REVERT: A 193 MET cc_start: 0.8824 (tpt) cc_final: 0.8509 (tpp) REVERT: A 276 PHE cc_start: 0.7930 (m-10) cc_final: 0.6670 (t80) REVERT: A 369 ASN cc_start: 0.6916 (m110) cc_final: 0.6331 (p0) REVERT: A 370 LYS cc_start: 0.7990 (ttpt) cc_final: 0.7449 (tttm) REVERT: A 371 GLU cc_start: 0.7611 (mp0) cc_final: 0.7332 (mp0) REVERT: D 57 GLU cc_start: 0.7713 (mp0) cc_final: 0.7349 (pm20) REVERT: D 119 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7388 (tp30) REVERT: D 194 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8309 (ttpp) REVERT: D 276 PHE cc_start: 0.7451 (t80) cc_final: 0.7175 (t80) REVERT: D 355 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7377 (ttt180) REVERT: D 369 ASN cc_start: 0.6744 (m110) cc_final: 0.6268 (p0) REVERT: D 370 LYS cc_start: 0.8021 (ttpt) cc_final: 0.7413 (ttpp) REVERT: D 372 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7478 (mt-10) REVERT: E 51 ARG cc_start: 0.7960 (mmt-90) cc_final: 0.7451 (mmt180) REVERT: E 61 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7304 (mmp) REVERT: E 119 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7504 (tp30) REVERT: E 276 PHE cc_start: 0.7638 (t80) cc_final: 0.6815 (m-80) REVERT: E 370 LYS cc_start: 0.7931 (ttpt) cc_final: 0.7354 (ttpp) outliers start: 43 outliers final: 18 residues processed: 224 average time/residue: 1.5852 time to fit residues: 394.0477 Evaluate side-chains 219 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 36 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.080827 restraints weight = 20142.723| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.66 r_work: 0.2870 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1403 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= 0.136 Angle : 0.503 7.349 22565 Z= 0.263 Chirality : 0.038 0.150 2385 Planarity : 0.004 0.034 2770 Dihedral : 12.375 121.079 2650 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.18 % Allowed : 10.38 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.19), residues: 1870 helix: 1.68 (0.14), residues: 1245 sheet: None (None), residues: 0 loop : 0.35 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 309 HIS 0.004 0.001 HIS C 178 PHE 0.016 0.001 PHE C 248 TYR 0.020 0.001 TYR E 97 ARG 0.005 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.05751 ( 975) hydrogen bonds : angle 4.27848 ( 2850) SS BOND : angle 0.00000 ( 5) covalent geometry : bond 0.00294 (16735) covalent geometry : angle 0.50294 (22560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 1.710 Fit side-chains REVERT: B 119 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7879 (tp30) REVERT: C 119 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: C 193 MET cc_start: 0.8860 (tpt) cc_final: 0.8563 (tpp) REVERT: C 355 ARG cc_start: 0.8048 (ttp-170) cc_final: 0.7751 (ttt90) REVERT: C 369 ASN cc_start: 0.6795 (m110) cc_final: 0.6096 (p0) REVERT: C 372 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7532 (mt-10) REVERT: A 193 MET cc_start: 0.8827 (tpt) cc_final: 0.8515 (tpp) REVERT: A 276 PHE cc_start: 0.7883 (m-10) cc_final: 0.6663 (t80) REVERT: A 340 LYS cc_start: 0.7628 (mptt) cc_final: 0.7422 (mptt) REVERT: A 369 ASN cc_start: 0.6953 (m110) cc_final: 0.6395 (p0) REVERT: A 370 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7405 (tttm) REVERT: A 371 GLU cc_start: 0.7630 (mp0) cc_final: 0.7335 (mp0) REVERT: D 119 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7380 (tp30) REVERT: D 194 LYS cc_start: 0.8549 (ttmt) cc_final: 0.8287 (ttpp) REVERT: D 262 LYS cc_start: 0.7644 (mmmm) cc_final: 0.7397 (mmmt) REVERT: D 276 PHE cc_start: 0.7536 (t80) cc_final: 0.7234 (t80) REVERT: D 369 ASN cc_start: 0.6736 (OUTLIER) cc_final: 0.6153 (p0) REVERT: D 370 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7494 (ttpp) REVERT: D 372 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7319 (mt-10) REVERT: E 25 ARG cc_start: 0.8075 (mtp85) cc_final: 0.7867 (mtp-110) REVERT: E 51 ARG cc_start: 0.7961 (mmt-90) cc_final: 0.7444 (mmt180) REVERT: E 61 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7296 (mmp) REVERT: E 119 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7450 (tp30) REVERT: E 276 PHE cc_start: 0.7583 (t80) cc_final: 0.7312 (t80) REVERT: E 369 ASN cc_start: 0.6728 (m110) cc_final: 0.6233 (p0) REVERT: E 370 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7342 (ttpp) outliers start: 37 outliers final: 17 residues processed: 232 average time/residue: 1.4211 time to fit residues: 362.3600 Evaluate side-chains 229 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 369 ASN 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 249 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 163 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN C 178 HIS ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.110781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.079721 restraints weight = 20364.462| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.67 r_work: 0.2850 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16735 Z= 0.157 Angle : 0.522 7.370 22565 Z= 0.272 Chirality : 0.040 0.150 2385 Planarity : 0.004 0.035 2770 Dihedral : 12.042 119.179 2646 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.06 % Allowed : 11.09 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.19), residues: 1870 helix: 1.67 (0.14), residues: 1245 sheet: None (None), residues: 0 loop : 0.36 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 309 HIS 0.005 0.001 HIS D 326 PHE 0.019 0.001 PHE C 248 TYR 0.022 0.002 TYR D 97 ARG 0.006 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.06035 ( 975) hydrogen bonds : angle 4.33172 ( 2850) SS BOND : angle 0.00000 ( 5) covalent geometry : bond 0.00352 (16735) covalent geometry : angle 0.52164 (22560) *********************** 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 244 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 2.210 Fit side-chains REVERT: B 72 TYR cc_start: 0.6386 (m-80) cc_final: 0.6178 (m-80) REVERT: B 119 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7890 (tp30) REVERT: C 119 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: C 193 MET cc_start: 0.8852 (tpt) cc_final: 0.8551 (tpp) REVERT: C 355 ARG cc_start: 0.8037 (ttp-170) cc_final: 0.7727 (ttt90) REVERT: A 193 MET cc_start: 0.8832 (tpt) cc_final: 0.8523 (tpp) REVERT: A 276 PHE cc_start: 0.7852 (m-10) cc_final: 0.6648 (t80) REVERT: A 340 LYS cc_start: 0.7632 (mptt) cc_final: 0.7420 (mptt) REVERT: A 369 ASN cc_start: 0.6998 (m110) cc_final: 0.6438 (p0) REVERT: A 370 LYS cc_start: 0.7824 (ttpt) cc_final: 0.7259 (tttm) REVERT: A 371 GLU cc_start: 0.7651 (mp0) cc_final: 0.7382 (mp0) REVERT: D 57 GLU cc_start: 0.7736 (mp0) cc_final: 0.7316 (pm20) REVERT: D 119 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7438 (tp30) REVERT: D 194 LYS cc_start: 0.8544 (ttmt) cc_final: 0.8276 (ttpp) REVERT: D 276 PHE cc_start: 0.7567 (t80) cc_final: 0.7285 (t80) REVERT: D 369 ASN cc_start: 0.6670 (OUTLIER) cc_final: 0.6089 (p0) REVERT: D 370 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7532 (ttpp) REVERT: D 372 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7334 (mt-10) REVERT: E 25 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7860 (mtp-110) REVERT: E 51 ARG cc_start: 0.7959 (mmt-90) cc_final: 0.7641 (mpt90) REVERT: E 61 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7308 (mmp) REVERT: E 119 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: E 276 PHE cc_start: 0.7599 (t80) cc_final: 0.7352 (t80) REVERT: E 369 ASN cc_start: 0.6791 (m110) cc_final: 0.6270 (p0) REVERT: E 370 LYS cc_start: 0.7890 (ttpt) cc_final: 0.7368 (ttpp) outliers start: 35 outliers final: 19 residues processed: 230 average time/residue: 1.8202 time to fit residues: 459.7178 Evaluate side-chains 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 2.765 ------------------------------------------------------------------------------- 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 205 ILE 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 369 ASN Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 110 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 178 optimal weight: 0.0570 chunk 85 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN C 178 HIS ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.112948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.082282 restraints weight = 20272.861| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.66 r_work: 0.2895 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16735 Z= 0.123 Angle : 0.487 7.099 22565 Z= 0.252 Chirality : 0.038 0.148 2385 Planarity : 0.004 0.033 2770 Dihedral : 11.595 116.863 2646 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.65 % Allowed : 11.74 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.19), residues: 1870 helix: 1.72 (0.14), residues: 1245 sheet: None (None), residues: 0 loop : 0.29 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 309 HIS 0.003 0.001 HIS E 178 PHE 0.014 0.001 PHE C 276 TYR 0.018 0.001 TYR D 97 ARG 0.006 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.05455 ( 975) hydrogen bonds : angle 4.22994 ( 2850) SS BOND : angle 0.00000 ( 5) covalent geometry : bond 0.00259 (16735) covalent geometry : angle 0.48690 (22560) *********************** 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 244 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 1.739 Fit side-chains REVERT: B 119 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7887 (tp30) REVERT: B 262 LYS cc_start: 0.7359 (mptp) cc_final: 0.7114 (mmmt) REVERT: B 355 ARG cc_start: 0.7963 (ttm-80) cc_final: 0.7726 (ttt180) REVERT: C 119 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: C 193 MET cc_start: 0.8853 (tpt) cc_final: 0.8563 (tpp) REVERT: C 355 ARG cc_start: 0.8041 (ttp-170) cc_final: 0.7629 (ttt90) REVERT: C 369 ASN cc_start: 0.6781 (m110) cc_final: 0.6477 (m110) REVERT: A 193 MET cc_start: 0.8828 (tpt) cc_final: 0.8527 (tpp) REVERT: A 276 PHE cc_start: 0.7863 (m-10) cc_final: 0.6652 (t80) REVERT: A 340 LYS cc_start: 0.7616 (mptt) cc_final: 0.7406 (mptt) REVERT: A 369 ASN cc_start: 0.6988 (m110) cc_final: 0.6491 (p0) REVERT: A 370 LYS cc_start: 0.7863 (ttpt) cc_final: 0.7336 (tttm) REVERT: A 371 GLU cc_start: 0.7653 (mp0) cc_final: 0.7376 (mp0) REVERT: D 57 GLU cc_start: 0.7765 (mp0) cc_final: 0.7315 (pm20) REVERT: D 119 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7425 (tp30) REVERT: D 194 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8258 (ttpp) REVERT: D 276 PHE cc_start: 0.7592 (t80) cc_final: 0.7326 (t80) REVERT: D 369 ASN cc_start: 0.6637 (OUTLIER) cc_final: 0.6104 (p0) REVERT: D 370 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7708 (ttpp) REVERT: D 371 GLU cc_start: 0.7535 (mp0) cc_final: 0.7220 (mp0) REVERT: E 51 ARG cc_start: 0.7928 (mmt-90) cc_final: 0.7599 (mpt90) REVERT: E 61 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7344 (mmp) REVERT: E 119 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: E 276 PHE cc_start: 0.7452 (t80) cc_final: 0.7231 (t80) REVERT: E 369 ASN cc_start: 0.6772 (m110) cc_final: 0.6306 (p0) REVERT: E 370 LYS cc_start: 0.7930 (ttpt) cc_final: 0.7383 (ttpp) outliers start: 28 outliers final: 16 residues processed: 231 average time/residue: 1.5093 time to fit residues: 381.9978 Evaluate side-chains 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 1.864 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 176 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.080083 restraints weight = 20204.923| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.65 r_work: 0.2858 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1551 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 7.209 22565 Z= 0.270 Chirality : 0.040 0.152 2385 Planarity : 0.004 0.044 2770 Dihedral : 11.548 117.465 2644 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.77 % Allowed : 11.98 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.19), residues: 1870 helix: 1.71 (0.14), residues: 1245 sheet: None (None), residues: 0 loop : 0.31 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 309 HIS 0.004 0.001 HIS D 326 PHE 0.027 0.001 PHE A 80 TYR 0.022 0.002 TYR D 97 ARG 0.007 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.05946 ( 975) hydrogen bonds : angle 4.30222 ( 2850) SS BOND : angle 0.00000 ( 5) covalent geometry : bond 0.00349 (16735) covalent geometry : angle 0.52144 (22560) *********************** 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: 30 poor density : 212 time to evaluate : 1.661 Fit side-chains REVERT: B 61 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7790 (tpp) REVERT: B 119 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7890 (tp30) REVERT: B 262 LYS cc_start: 0.7368 (mptp) cc_final: 0.7119 (mmmt) REVERT: C 119 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: C 193 MET cc_start: 0.8860 (tpt) cc_final: 0.8561 (tpp) REVERT: C 355 ARG cc_start: 0.8029 (ttp-170) cc_final: 0.7729 (ttt90) REVERT: A 193 MET cc_start: 0.8816 (tpt) cc_final: 0.8515 (tpp) REVERT: A 276 PHE cc_start: 0.7846 (m-10) cc_final: 0.6638 (t80) REVERT: A 340 LYS cc_start: 0.7618 (mptt) cc_final: 0.7391 (mptt) REVERT: A 369 ASN cc_start: 0.6973 (m110) cc_final: 0.6490 (p0) REVERT: A 370 LYS cc_start: 0.7821 (ttpt) cc_final: 0.7273 (tttm) REVERT: D 57 GLU cc_start: 0.7770 (mp0) cc_final: 0.7324 (pm20) REVERT: D 119 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7438 (tp30) REVERT: D 194 LYS cc_start: 0.8543 (ttmt) cc_final: 0.8277 (ttpp) REVERT: D 276 PHE cc_start: 0.7597 (t80) cc_final: 0.7359 (t80) REVERT: D 355 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7416 (ttt180) REVERT: D 370 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7650 (ttpp) REVERT: E 51 ARG cc_start: 0.7916 (mmt-90) cc_final: 0.7599 (mpt90) REVERT: E 61 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7344 (mmp) REVERT: E 119 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: E 276 PHE cc_start: 0.7583 (t80) cc_final: 0.7323 (t80) REVERT: E 369 ASN cc_start: 0.6832 (m110) cc_final: 0.6294 (p0) REVERT: E 370 LYS cc_start: 0.7911 (ttpt) cc_final: 0.7354 (ttpp) outliers start: 30 outliers final: 18 residues processed: 228 average time/residue: 1.4917 time to fit residues: 372.3614 Evaluate side-chains 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 169 LYS 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 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 126 optimal weight: 0.0050 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.110798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.079855 restraints weight = 20177.773| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.66 r_work: 0.2854 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16735 Z= 0.159 Angle : 0.529 7.665 22565 Z= 0.274 Chirality : 0.040 0.153 2385 Planarity : 0.004 0.045 2770 Dihedral : 11.504 118.455 2644 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.59 % Allowed : 12.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.19), residues: 1870 helix: 1.69 (0.14), residues: 1245 sheet: None (None), residues: 0 loop : 0.29 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 309 HIS 0.004 0.001 HIS D 326 PHE 0.020 0.001 PHE C 248 TYR 0.022 0.002 TYR D 97 ARG 0.007 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.06003 ( 975) hydrogen bonds : angle 4.32856 ( 2850) SS BOND : angle 0.00000 ( 5) covalent geometry : bond 0.00359 (16735) covalent geometry : angle 0.52915 (22560) *********************** 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: 27 poor density : 211 time to evaluate : 1.718 Fit side-chains REVERT: B 61 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7766 (tpp) REVERT: B 119 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7895 (tp30) REVERT: B 262 LYS cc_start: 0.7382 (mptp) cc_final: 0.7130 (mmmt) REVERT: C 119 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: C 193 MET cc_start: 0.8859 (tpt) cc_final: 0.8558 (tpp) REVERT: C 276 PHE cc_start: 0.7816 (m-80) cc_final: 0.6466 (t80) REVERT: C 355 ARG cc_start: 0.8030 (ttp-170) cc_final: 0.7725 (ttt90) REVERT: A 193 MET cc_start: 0.8820 (tpt) cc_final: 0.8518 (tpp) REVERT: A 276 PHE cc_start: 0.7860 (m-10) cc_final: 0.6641 (t80) REVERT: A 340 LYS cc_start: 0.7661 (mptt) cc_final: 0.7430 (mptt) REVERT: A 370 LYS cc_start: 0.7791 (ttpt) cc_final: 0.7240 (tttm) REVERT: D 57 GLU cc_start: 0.7772 (mp0) cc_final: 0.7338 (pm20) REVERT: D 119 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7452 (tp30) REVERT: D 194 LYS cc_start: 0.8527 (ttmt) cc_final: 0.8260 (ttpp) REVERT: D 276 PHE cc_start: 0.7611 (t80) cc_final: 0.7366 (t80) REVERT: D 355 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7411 (ttt180) REVERT: D 370 LYS cc_start: 0.8061 (ttpt) cc_final: 0.7595 (ttpp) REVERT: E 51 ARG cc_start: 0.7910 (mmt-90) cc_final: 0.7594 (mpt90) REVERT: E 61 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7320 (mmp) REVERT: E 119 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: E 276 PHE cc_start: 0.7622 (t80) cc_final: 0.7326 (t80) REVERT: E 370 LYS cc_start: 0.7904 (ttpt) cc_final: 0.7321 (ttpp) outliers start: 27 outliers final: 18 residues processed: 224 average time/residue: 1.5356 time to fit residues: 375.7651 Evaluate side-chains 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 205 ILE 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 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.111987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.081210 restraints weight = 20242.971| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.66 r_work: 0.2877 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1655 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 : 0.513 8.916 22565 Z= 0.263 Chirality : 0.039 0.195 2385 Planarity : 0.004 0.044 2770 Dihedral : 11.197 118.168 2644 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.19), residues: 1870 helix: 1.72 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : 0.25 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 309 HIS 0.004 0.001 HIS C 178 PHE 0.017 0.001 PHE C 248 TYR 0.020 0.001 TYR D 97 ARG 0.008 0.000 ARG C 51 Details of bonding type rmsd hydrogen bonds : bond 0.05662 ( 975) hydrogen bonds : angle 4.28873 ( 2850) SS BOND : angle 0.00000 ( 5) covalent geometry : bond 0.00293 (16735) covalent geometry : angle 0.51293 (22560) *********************** 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 242 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 1.762 Fit side-chains REVERT: B 61 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7766 (tpp) REVERT: B 119 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7887 (tp30) REVERT: B 355 ARG cc_start: 0.7968 (ttm-80) cc_final: 0.7739 (ttt180) REVERT: C 119 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: C 193 MET cc_start: 0.8857 (tpt) cc_final: 0.8563 (tpp) REVERT: C 276 PHE cc_start: 0.7801 (m-80) cc_final: 0.6468 (t80) REVERT: C 355 ARG cc_start: 0.8040 (ttp-170) cc_final: 0.7613 (ttt90) REVERT: C 369 ASN cc_start: 0.6748 (m110) cc_final: 0.6456 (m110) REVERT: A 193 MET cc_start: 0.8817 (tpt) cc_final: 0.8519 (tpp) REVERT: A 276 PHE cc_start: 0.7883 (m-10) cc_final: 0.6648 (t80) REVERT: A 370 LYS cc_start: 0.7777 (ttpt) cc_final: 0.7210 (tttm) REVERT: D 57 GLU cc_start: 0.7770 (mp0) cc_final: 0.7332 (pm20) REVERT: D 119 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7443 (tp30) REVERT: D 194 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8304 (ttpp) REVERT: D 276 PHE cc_start: 0.7599 (t80) cc_final: 0.7370 (t80) REVERT: D 355 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7399 (ttt180) REVERT: D 370 LYS cc_start: 0.8050 (ttpt) cc_final: 0.7576 (ttpp) REVERT: E 51 ARG cc_start: 0.7928 (mmt-90) cc_final: 0.7604 (mpt90) REVERT: E 61 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7335 (mmp) REVERT: E 119 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: E 276 PHE cc_start: 0.7525 (t80) cc_final: 0.7272 (t80) REVERT: E 369 ASN cc_start: 0.6838 (m110) cc_final: 0.6247 (p0) REVERT: E 370 LYS cc_start: 0.7895 (ttpt) cc_final: 0.7322 (ttpp) REVERT: E 372 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7577 (mt-10) outliers start: 29 outliers final: 19 residues processed: 228 average time/residue: 1.5091 time to fit residues: 376.3723 Evaluate side-chains 233 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 205 ILE 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 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 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 121 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.112022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.081263 restraints weight = 20274.121| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.66 r_work: 0.2878 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1686 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= 0.134 Angle : 0.519 9.823 22565 Z= 0.264 Chirality : 0.039 0.238 2385 Planarity : 0.004 0.034 2770 Dihedral : 10.901 116.978 2644 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.65 % Allowed : 12.33 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.19), residues: 1870 helix: 1.70 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : 0.24 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 309 HIS 0.004 0.001 HIS E 178 PHE 0.016 0.001 PHE C 248 TYR 0.020 0.001 TYR D 97 ARG 0.008 0.000 ARG C 51 Details of bonding type rmsd hydrogen bonds : bond 0.05659 ( 975) hydrogen bonds : angle 4.29705 ( 2850) SS BOND : angle 0.00000 ( 5) covalent geometry : bond 0.00291 (16735) covalent geometry : angle 0.51908 (22560) ********************** 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 241 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 1.944 Fit side-chains REVERT: B 119 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7882 (tp30) REVERT: B 262 LYS cc_start: 0.7441 (mptp) cc_final: 0.7062 (mmmt) REVERT: B 355 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7766 (ttt180) REVERT: C 119 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: C 193 MET cc_start: 0.8858 (tpt) cc_final: 0.8562 (tpp) REVERT: C 355 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.7586 (ttt90) REVERT: C 369 ASN cc_start: 0.6627 (m110) cc_final: 0.6201 (m110) REVERT: C 372 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7409 (mt-10) REVERT: A 193 MET cc_start: 0.8813 (tpt) cc_final: 0.8511 (tpp) REVERT: A 276 PHE cc_start: 0.7880 (m-10) cc_final: 0.6647 (t80) REVERT: A 370 LYS cc_start: 0.7771 (ttpt) cc_final: 0.7213 (tttm) REVERT: D 57 GLU cc_start: 0.7715 (mp0) cc_final: 0.7282 (pm20) REVERT: D 119 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7441 (tp30) REVERT: D 194 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8311 (ttpp) REVERT: D 276 PHE cc_start: 0.7599 (t80) cc_final: 0.7372 (t80) REVERT: D 355 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7380 (ttt180) REVERT: D 370 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7572 (ttpp) REVERT: E 51 ARG cc_start: 0.7935 (mmt-90) cc_final: 0.7618 (mpt90) REVERT: E 61 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7327 (mmp) REVERT: E 119 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: E 369 ASN cc_start: 0.6823 (m110) cc_final: 0.6299 (p0) REVERT: E 370 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7331 (ttpp) outliers start: 28 outliers final: 21 residues processed: 227 average time/residue: 1.7723 time to fit residues: 440.1419 Evaluate side-chains 238 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain 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 76 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 205 ILE 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 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 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 165 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.0270 chunk 154 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.111446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.080677 restraints weight = 20242.375| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.65 r_work: 0.2869 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1664 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= 0.144 Angle : 0.531 10.760 22565 Z= 0.270 Chirality : 0.040 0.256 2385 Planarity : 0.004 0.034 2770 Dihedral : 10.790 117.041 2644 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.47 % Allowed : 12.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.19), residues: 1870 helix: 1.68 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : 0.23 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 309 HIS 0.004 0.001 HIS E 178 PHE 0.017 0.001 PHE C 248 TYR 0.021 0.001 TYR D 97 ARG 0.007 0.000 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.05789 ( 975) hydrogen bonds : angle 4.32805 ( 2850) SS BOND : angle 0.00000 ( 5) covalent geometry : bond 0.00316 (16735) covalent geometry : angle 0.53131 (22560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15365.13 seconds wall clock time: 267 minutes 29.13 seconds (16049.13 seconds total)