Starting phenix.real_space_refine on Sat May 17 10:33:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dym_47309/05_2025/9dym_47309.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dym_47309/05_2025/9dym_47309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dym_47309/05_2025/9dym_47309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dym_47309/05_2025/9dym_47309.map" model { file = "/net/cci-nas-00/data/ceres_data/9dym_47309/05_2025/9dym_47309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dym_47309/05_2025/9dym_47309.cif" } resolution = 2.67 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= 0.004 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 S 80 5.16 5 Cl 2 4.86 5 C 10281 2.51 5 N 2553 2.21 5 O 2708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15629 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "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: "E" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "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: "C" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' CA': 1, 'PAB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CA': 1, ' CL': 1, 'PAB': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' CL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' CA': 1, 'PAB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.93, per 1000 atoms: 0.64 Number of scatterers: 15629 At special positions: 0 Unit cell: (106.24, 107.9, 112.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 Cl 2 17.00 S 80 16.00 O 2708 8.00 N 2553 7.00 C 10281 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.71 Conformation dependent library (CDL) restraints added in 1.9 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: 83 helices and 5 sheets defined 69.5% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'D' and resid 18 through 23 removed outlier: 3.541A pdb=" N LEU D 22 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.645A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 71 removed outlier: 3.945A pdb=" N SER D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) 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: 3.674A 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: 3.836A pdb=" N LEU D 252 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 4.126A 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 Processing helix chain 'D' and resid 306 through 324 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 370 through 373 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.678A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 71 removed outlier: 4.157A pdb=" N SER B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 removed outlier: 4.348A pdb=" N ILE B 78 " --> pdb=" O GLN B 74 " (cutoff:3.500A) 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: 3.627A 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: 4.043A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.701A 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 'E' and resid 18 through 23 Processing helix chain 'E' and resid 27 through 53 removed outlier: 5.647A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 99 removed outlier: 3.763A pdb=" N VAL E 81 " --> pdb=" O PRO E 77 " (cutoff:3.500A) 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: 3.659A 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: 3.823A pdb=" N LEU E 252 " --> pdb=" O PHE E 248 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.732A 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 helix chain 'E' and resid 370 through 373 Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.521A pdb=" N LEU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 52 removed outlier: 5.677A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 73 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 78 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: 3.672A 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: 4.029A 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: 3.686A 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 'C' and resid 18 through 23 Processing helix chain 'C' and resid 27 through 53 removed outlier: 5.741A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.795A 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 73 through 76 Processing helix chain 'C' and resid 77 through 99 removed outlier: 3.562A pdb=" N LEU C 88 " --> pdb=" O PHE C 84 " (cutoff:3.500A) 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: 3.661A 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: 3.788A pdb=" N LEU C 252 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 4.069A 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: 3.721A 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 sheet with id=AA1, first strand: chain 'D' and resid 347 through 348 removed outlier: 4.326A pdb=" N TYR D 347 " --> pdb=" O GLN E 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 375 through 376 removed outlier: 4.267A pdb=" N TYR C 347 " --> pdb=" O GLN D 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.537A pdb=" N TYR B 347 " --> pdb=" O GLN C 376 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 375 through 376 removed outlier: 4.546A pdb=" N TYR A 347 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 347 through 348 removed outlier: 4.565A pdb=" N TYR E 347 " --> pdb=" O GLN A 376 " (cutoff:3.500A) 963 hydrogen bonds defined for protein. 2793 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: 4.75 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3127 1.32 - 1.46: 4218 1.46 - 1.59: 8615 1.59 - 1.73: 0 1.73 - 1.87: 135 Bond restraints: 16095 Sorted by residual: bond pdb=" C GLU E 213 " pdb=" O GLU E 213 " ideal model delta sigma weight residual 1.237 1.299 -0.063 1.16e-02 7.43e+03 2.91e+01 bond pdb=" C GLY B 135 " pdb=" O GLY B 135 " ideal model delta sigma weight residual 1.234 1.296 -0.063 1.20e-02 6.94e+03 2.73e+01 bond pdb=" C ARG D 105 " pdb=" O ARG D 105 " ideal model delta sigma weight residual 1.237 1.294 -0.057 1.16e-02 7.43e+03 2.45e+01 bond pdb=" C PHE C 80 " pdb=" O PHE C 80 " ideal model delta sigma weight residual 1.237 1.293 -0.057 1.16e-02 7.43e+03 2.40e+01 bond pdb=" C ARG B 105 " pdb=" O ARG B 105 " ideal model delta sigma weight residual 1.237 1.292 -0.055 1.16e-02 7.43e+03 2.28e+01 ... (remaining 16090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 17535 1.67 - 3.33: 4094 3.33 - 5.00: 263 5.00 - 6.67: 27 6.67 - 8.34: 5 Bond angle restraints: 21924 Sorted by residual: angle pdb=" C PRO B 77 " pdb=" CA PRO B 77 " pdb=" CB PRO B 77 " ideal model delta sigma weight residual 112.62 105.46 7.16 1.65e+00 3.67e-01 1.88e+01 angle pdb=" C PRO D 260 " pdb=" N ALA D 261 " pdb=" CA ALA D 261 " ideal model delta sigma weight residual 120.38 126.31 -5.93 1.37e+00 5.33e-01 1.87e+01 angle pdb=" N VAL D 290 " pdb=" CA VAL D 290 " pdb=" C VAL D 290 " ideal model delta sigma weight residual 110.42 106.34 4.08 9.60e-01 1.09e+00 1.81e+01 angle pdb=" CA ALA E 263 " pdb=" C ALA E 263 " pdb=" O ALA E 263 " ideal model delta sigma weight residual 120.57 115.48 5.09 1.20e+00 6.94e-01 1.80e+01 angle pdb=" N PRO E 77 " pdb=" CA PRO E 77 " pdb=" CB PRO E 77 " ideal model delta sigma weight residual 102.35 105.32 -2.97 7.10e-01 1.98e+00 1.75e+01 ... (remaining 21919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 8295 17.64 - 35.27: 798 35.27 - 52.90: 207 52.90 - 70.54: 53 70.54 - 88.17: 25 Dihedral angle restraints: 9378 sinusoidal: 3813 harmonic: 5565 Sorted by residual: dihedral pdb=" CD ARG E 51 " pdb=" NE ARG E 51 " pdb=" CZ ARG E 51 " pdb=" NH1 ARG E 51 " ideal model delta sinusoidal sigma weight residual 0.00 32.60 -32.60 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" CA GLY D 112 " pdb=" C GLY D 112 " pdb=" N PHE D 113 " pdb=" CA PHE D 113 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA LEU D 174 " pdb=" C LEU D 174 " pdb=" N SER D 175 " pdb=" CA SER D 175 " ideal model delta harmonic sigma weight residual -180.00 -161.28 -18.72 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 9375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1177 0.055 - 0.110: 835 0.110 - 0.165: 286 0.165 - 0.219: 66 0.219 - 0.274: 11 Chirality restraints: 2375 Sorted by residual: chirality pdb=" CG LEU D 60 " pdb=" CB LEU D 60 " pdb=" CD1 LEU D 60 " pdb=" CD2 LEU D 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CG LEU B 210 " pdb=" CB LEU B 210 " pdb=" CD1 LEU B 210 " pdb=" CD2 LEU B 210 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA LEU B 176 " pdb=" N LEU B 176 " pdb=" C LEU B 176 " pdb=" CB LEU B 176 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2372 not shown) Planarity restraints: 2756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 51 " 0.578 9.50e-02 1.11e+02 2.59e-01 4.11e+01 pdb=" NE ARG E 51 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG E 51 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG E 51 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 51 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 122 " -0.442 9.50e-02 1.11e+02 1.98e-01 2.40e+01 pdb=" NE ARG C 122 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG C 122 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 122 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 122 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 263 " -0.024 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C ALA E 263 " 0.084 2.00e-02 2.50e+03 pdb=" O ALA E 263 " -0.030 2.00e-02 2.50e+03 pdb=" N TYR E 264 " -0.030 2.00e-02 2.50e+03 ... (remaining 2753 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 207 2.65 - 3.21: 14368 3.21 - 3.78: 26585 3.78 - 4.34: 37074 4.34 - 4.90: 59338 Nonbonded interactions: 137572 Sorted by model distance: nonbonded pdb=" OG SER D 358 " pdb=" O PRO B 177 " model vdw 2.088 3.040 nonbonded pdb=" OE1 GLU E 292 " pdb=" OG SER A 16 " model vdw 2.090 3.040 nonbonded pdb=" O PRO D 177 " pdb=" OG SER A 358 " model vdw 2.154 3.040 nonbonded pdb=" N GLU E 57 " pdb=" OE1 GLU E 57 " model vdw 2.166 3.120 nonbonded pdb=" NH2 ARG A 51 " pdb=" O PHE A 257 " model vdw 2.193 3.120 ... (remaining 137567 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 601)) selection = (chain 'B' and (resid 2 through 377 or resid 601)) selection = chain 'C' selection = (chain 'D' and (resid 2 through 377 or resid 601)) selection = (chain 'E' and (resid 2 through 377 or resid 601)) } 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: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 35.640 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 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 : 0.013 0.081 16095 Z= 0.939 Angle : 1.313 8.335 21924 Z= 0.960 Chirality : 0.078 0.274 2375 Planarity : 0.011 0.259 2756 Dihedral : 15.934 88.173 5788 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.12 % Allowed : 9.73 % Favored : 88.14 % 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: 1.40 (0.18), residues: 1870 helix: 1.60 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : -0.21 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.012 TRP E 309 HIS 0.024 0.004 HIS C 168 PHE 0.050 0.010 PHE E 276 TYR 0.051 0.011 TYR A 44 ARG 0.043 0.004 ARG A 51 Details of bonding type rmsd hydrogen bonds : bond 0.15000 ( 963) hydrogen bonds : angle 5.36124 ( 2793) covalent geometry : bond 0.01320 (16095) covalent geometry : angle 1.31340 (21924) *********************** 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 213 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 1.667 Fit side-chains REVERT: D 61 MET cc_start: 0.7428 (mtt) cc_final: 0.7151 (ptt) REVERT: D 64 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7586 (tppt) REVERT: D 68 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.6820 (t80) REVERT: D 120 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8483 (tp40) REVERT: B 262 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6904 (mttt) REVERT: B 365 ASN cc_start: 0.8631 (m110) cc_final: 0.8379 (m-40) REVERT: A 57 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7946 (mp0) REVERT: A 203 ASP cc_start: 0.9129 (t70) cc_final: 0.8845 (t0) REVERT: C 203 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8526 (t70) REVERT: C 369 ASN cc_start: 0.7102 (m110) cc_final: 0.6660 (t0) REVERT: C 376 GLN cc_start: 0.7265 (mt0) cc_final: 0.6520 (mm110) outliers start: 36 outliers final: 9 residues processed: 202 average time/residue: 1.3861 time to fit residues: 307.9502 Evaluate side-chains 172 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 367 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 107 optimal weight: 0.1980 chunk 168 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 11 ASN D 208 GLN B 208 GLN E 159 GLN E 208 GLN E 296 ASN A 159 GLN A 208 GLN A 267 HIS A 369 ASN C 168 HIS C 208 GLN C 369 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.086927 restraints weight = 21846.944| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.73 r_work: 0.2923 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16095 Z= 0.128 Angle : 0.512 8.569 21924 Z= 0.271 Chirality : 0.038 0.186 2375 Planarity : 0.004 0.039 2756 Dihedral : 6.373 89.917 2107 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.89 % Allowed : 10.97 % Favored : 87.14 % 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: 1.57 (0.19), residues: 1870 helix: 1.71 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.20 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 309 HIS 0.004 0.001 HIS C 178 PHE 0.017 0.001 PHE A 248 TYR 0.019 0.001 TYR C 97 ARG 0.005 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.05668 ( 963) hydrogen bonds : angle 4.37225 ( 2793) covalent geometry : bond 0.00268 (16095) covalent geometry : angle 0.51173 (21924) *********************** 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 204 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 1.784 Fit side-chains REVERT: D 64 LYS cc_start: 0.7947 (mtmt) cc_final: 0.7304 (mmtm) REVERT: D 68 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6233 (t80) REVERT: D 203 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8065 (t70) REVERT: B 336 MET cc_start: 0.8883 (ttm) cc_final: 0.8503 (ttm) REVERT: B 365 ASN cc_start: 0.8558 (m110) cc_final: 0.8242 (m-40) REVERT: B 369 ASN cc_start: 0.7103 (m-40) cc_final: 0.6768 (m110) REVERT: E 214 MET cc_start: 0.8043 (tpt) cc_final: 0.6892 (tmm) REVERT: A 49 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7040 (mp) REVERT: C 46 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8342 (mp) REVERT: C 369 ASN cc_start: 0.6837 (m-40) cc_final: 0.6335 (t0) outliers start: 32 outliers final: 9 residues processed: 193 average time/residue: 1.3104 time to fit residues: 279.4935 Evaluate side-chains 167 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 35 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 174 optimal weight: 6.9990 chunk 177 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 376 GLN C 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.086707 restraints weight = 21861.639| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.72 r_work: 0.2927 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16095 Z= 0.134 Angle : 0.489 8.438 21924 Z= 0.258 Chirality : 0.038 0.153 2375 Planarity : 0.004 0.040 2756 Dihedral : 5.506 89.785 2089 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.12 % Allowed : 12.27 % Favored : 85.60 % 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: 1.58 (0.19), residues: 1870 helix: 1.73 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.22 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 309 HIS 0.004 0.001 HIS C 178 PHE 0.019 0.001 PHE A 248 TYR 0.027 0.001 TYR C 97 ARG 0.006 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.05396 ( 963) hydrogen bonds : angle 4.26448 ( 2793) covalent geometry : bond 0.00296 (16095) covalent geometry : angle 0.48947 (21924) *********************** 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 201 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 1.705 Fit side-chains revert: symmetry clash REVERT: D 64 LYS cc_start: 0.8048 (mtmt) cc_final: 0.7395 (mmtm) REVERT: D 68 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6391 (t80) REVERT: D 76 ILE cc_start: 0.6741 (OUTLIER) cc_final: 0.6460 (mp) REVERT: D 203 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8100 (t70) REVERT: D 333 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8233 (pt0) REVERT: D 374 GLU cc_start: 0.7398 (pm20) cc_final: 0.6980 (pm20) REVERT: B 75 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6991 (pp) REVERT: B 336 MET cc_start: 0.8870 (ttm) cc_final: 0.8492 (ttm) REVERT: B 369 ASN cc_start: 0.7218 (m-40) cc_final: 0.6826 (m110) REVERT: A 49 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7071 (mp) REVERT: C 46 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8349 (mp) outliers start: 36 outliers final: 13 residues processed: 188 average time/residue: 1.2862 time to fit residues: 267.6399 Evaluate side-chains 165 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 182 optimal weight: 6.9990 chunk 2 optimal weight: 0.0980 chunk 144 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.104959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.086213 restraints weight = 21874.231| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.71 r_work: 0.2921 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16095 Z= 0.141 Angle : 0.489 8.344 21924 Z= 0.257 Chirality : 0.038 0.153 2375 Planarity : 0.004 0.041 2756 Dihedral : 5.419 87.631 2089 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.60 % Allowed : 12.51 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.19), residues: 1870 helix: 1.59 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.38 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 309 HIS 0.004 0.001 HIS C 178 PHE 0.020 0.001 PHE A 248 TYR 0.022 0.001 TYR C 97 ARG 0.006 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.05370 ( 963) hydrogen bonds : angle 4.23095 ( 2793) covalent geometry : bond 0.00318 (16095) covalent geometry : angle 0.48938 (21924) *********************** 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 202 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 1.710 Fit side-chains revert: symmetry clash REVERT: D 68 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6479 (t80) REVERT: D 76 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6480 (mp) REVERT: D 203 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8104 (t70) REVERT: D 333 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8233 (pt0) REVERT: D 374 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: B 75 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7040 (pp) REVERT: B 336 MET cc_start: 0.8876 (ttm) cc_final: 0.8478 (ttm) REVERT: B 369 ASN cc_start: 0.7091 (m-40) cc_final: 0.6761 (m110) REVERT: E 57 GLU cc_start: 0.6416 (pm20) cc_final: 0.5705 (tt0) REVERT: E 70 ASP cc_start: 0.7493 (t0) cc_final: 0.7158 (t0) REVERT: E 214 MET cc_start: 0.8069 (tpt) cc_final: 0.6931 (tmm) REVERT: A 49 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7085 (mp) REVERT: C 46 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8352 (mp) outliers start: 44 outliers final: 18 residues processed: 190 average time/residue: 1.2577 time to fit residues: 264.5911 Evaluate side-chains 173 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 107 optimal weight: 0.0570 chunk 99 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.090429 restraints weight = 22285.311| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.67 r_work: 0.2994 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16095 Z= 0.111 Angle : 0.457 8.063 21924 Z= 0.240 Chirality : 0.036 0.150 2375 Planarity : 0.004 0.041 2756 Dihedral : 5.261 86.457 2089 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.54 % Allowed : 12.98 % Favored : 84.48 % 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: 1.50 (0.19), residues: 1870 helix: 1.67 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.37 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 309 HIS 0.003 0.001 HIS C 178 PHE 0.015 0.001 PHE A 248 TYR 0.026 0.001 TYR C 97 ARG 0.004 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.04925 ( 963) hydrogen bonds : angle 4.14910 ( 2793) covalent geometry : bond 0.00231 (16095) covalent geometry : angle 0.45704 (21924) *********************** 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 205 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.746 Fit side-chains revert: symmetry clash REVERT: D 68 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6486 (t80) REVERT: D 76 ILE cc_start: 0.6916 (OUTLIER) cc_final: 0.6620 (mp) REVERT: D 120 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7851 (tp40) REVERT: D 203 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8085 (t70) REVERT: D 374 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7347 (pm20) REVERT: B 75 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7093 (pp) REVERT: B 336 MET cc_start: 0.8884 (ttm) cc_final: 0.8418 (ttm) REVERT: B 369 ASN cc_start: 0.7140 (m-40) cc_final: 0.6811 (m110) REVERT: E 70 ASP cc_start: 0.7564 (t0) cc_final: 0.7249 (t0) REVERT: E 74 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: A 49 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7138 (mp) REVERT: C 46 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8418 (mp) outliers start: 43 outliers final: 19 residues processed: 192 average time/residue: 1.2276 time to fit residues: 261.7280 Evaluate side-chains 174 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 184 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN C 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.102576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.083660 restraints weight = 22155.289| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.72 r_work: 0.2871 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16095 Z= 0.214 Angle : 0.546 8.548 21924 Z= 0.287 Chirality : 0.041 0.158 2375 Planarity : 0.004 0.045 2756 Dihedral : 5.472 86.579 2089 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.54 % Allowed : 13.63 % Favored : 83.83 % 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: 1.25 (0.19), residues: 1870 helix: 1.46 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.42 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 309 HIS 0.007 0.001 HIS C 178 PHE 0.026 0.002 PHE A 248 TYR 0.028 0.002 TYR C 97 ARG 0.010 0.001 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.06016 ( 963) hydrogen bonds : angle 4.30373 ( 2793) covalent geometry : bond 0.00511 (16095) covalent geometry : angle 0.54610 (21924) *********************** 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 193 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 1.728 Fit side-chains revert: symmetry clash REVERT: D 68 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6482 (t80) REVERT: D 76 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6662 (mp) REVERT: D 203 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8138 (t70) REVERT: D 374 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7352 (pm20) REVERT: B 75 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7057 (pp) REVERT: B 336 MET cc_start: 0.8895 (ttm) cc_final: 0.8646 (ttp) REVERT: B 369 ASN cc_start: 0.7105 (m-40) cc_final: 0.6796 (m110) REVERT: E 70 ASP cc_start: 0.7569 (t0) cc_final: 0.7250 (t0) REVERT: E 214 MET cc_start: 0.8137 (tpt) cc_final: 0.7032 (tmm) REVERT: A 49 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7062 (mp) REVERT: C 46 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8344 (mp) REVERT: C 74 GLN cc_start: 0.8247 (pm20) cc_final: 0.7947 (pm20) outliers start: 43 outliers final: 16 residues processed: 179 average time/residue: 1.2553 time to fit residues: 249.2216 Evaluate side-chains 165 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 54 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.085157 restraints weight = 22002.188| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.72 r_work: 0.2905 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16095 Z= 0.157 Angle : 0.504 8.373 21924 Z= 0.266 Chirality : 0.038 0.153 2375 Planarity : 0.004 0.042 2756 Dihedral : 5.407 87.153 2089 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.30 % Allowed : 13.86 % Favored : 83.83 % 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: 1.25 (0.19), residues: 1870 helix: 1.48 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.46 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 309 HIS 0.004 0.001 HIS C 178 PHE 0.022 0.001 PHE A 248 TYR 0.024 0.001 TYR C 97 ARG 0.010 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.05516 ( 963) hydrogen bonds : angle 4.25976 ( 2793) covalent geometry : bond 0.00362 (16095) covalent geometry : angle 0.50414 (21924) *********************** 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 189 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 2.062 Fit side-chains revert: symmetry clash REVERT: D 68 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6619 (t80) REVERT: D 76 ILE cc_start: 0.6981 (OUTLIER) cc_final: 0.6652 (mp) REVERT: D 203 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8076 (t70) REVERT: D 374 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: B 75 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7045 (pp) REVERT: B 336 MET cc_start: 0.8888 (ttm) cc_final: 0.8440 (ttm) REVERT: B 369 ASN cc_start: 0.7089 (m-40) cc_final: 0.6761 (m110) REVERT: E 70 ASP cc_start: 0.7547 (t0) cc_final: 0.7218 (t0) REVERT: E 214 MET cc_start: 0.8091 (tpt) cc_final: 0.6956 (tmm) REVERT: A 49 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7065 (mp) REVERT: C 46 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8293 (mp) REVERT: C 74 GLN cc_start: 0.8269 (pm20) cc_final: 0.8005 (pm20) REVERT: C 360 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.7131 (mmm) outliers start: 39 outliers final: 19 residues processed: 180 average time/residue: 1.2713 time to fit residues: 253.4105 Evaluate side-chains 169 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 360 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 63 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 74 optimal weight: 0.0370 overall best weight: 1.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.084180 restraints weight = 22112.330| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.74 r_work: 0.2888 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16095 Z= 0.184 Angle : 0.525 8.466 21924 Z= 0.277 Chirality : 0.040 0.155 2375 Planarity : 0.004 0.043 2756 Dihedral : 5.442 87.211 2089 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.30 % Allowed : 13.98 % Favored : 83.72 % 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: 1.37 (0.19), residues: 1870 helix: 1.56 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.30 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 309 HIS 0.005 0.001 HIS C 178 PHE 0.023 0.002 PHE A 248 TYR 0.024 0.002 TYR C 97 ARG 0.012 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.05750 ( 963) hydrogen bonds : angle 4.29115 ( 2793) covalent geometry : bond 0.00434 (16095) covalent geometry : angle 0.52503 (21924) *********************** 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 183 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 1.893 Fit side-chains revert: symmetry clash REVERT: D 68 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.6527 (t80) REVERT: D 76 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6750 (mp) REVERT: D 120 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7897 (tp40) REVERT: D 203 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8119 (t70) REVERT: D 374 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7372 (pm20) REVERT: B 75 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7158 (pp) REVERT: B 336 MET cc_start: 0.8927 (ttm) cc_final: 0.8462 (ttm) REVERT: E 70 ASP cc_start: 0.7585 (t0) cc_final: 0.7257 (t0) REVERT: E 74 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7632 (pp30) REVERT: E 214 MET cc_start: 0.8172 (tpt) cc_final: 0.7091 (tmm) REVERT: A 49 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7148 (mp) REVERT: C 46 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8386 (mp) REVERT: C 74 GLN cc_start: 0.8294 (pm20) cc_final: 0.7958 (pm20) REVERT: C 360 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.7254 (mmm) REVERT: C 371 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7107 (pm20) outliers start: 39 outliers final: 20 residues processed: 174 average time/residue: 1.4042 time to fit residues: 270.3343 Evaluate side-chains 170 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain D residue 303 ASP Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 360 MET Chi-restraints excluded: chain C residue 371 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 124 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.087366 restraints weight = 22200.336| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.70 r_work: 0.2947 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16095 Z= 0.143 Angle : 0.495 8.259 21924 Z= 0.260 Chirality : 0.038 0.152 2375 Planarity : 0.004 0.047 2756 Dihedral : 5.338 86.393 2089 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.06 % Allowed : 14.28 % Favored : 83.66 % 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: 1.27 (0.19), residues: 1870 helix: 1.51 (0.14), residues: 1255 sheet: None (None), residues: 0 loop : -0.49 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 309 HIS 0.004 0.001 HIS C 178 PHE 0.020 0.001 PHE A 248 TYR 0.022 0.001 TYR C 97 ARG 0.013 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.05340 ( 963) hydrogen bonds : angle 4.23980 ( 2793) covalent geometry : bond 0.00324 (16095) covalent geometry : angle 0.49495 (21924) *********************** 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 184 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 1.904 Fit side-chains revert: symmetry clash REVERT: D 68 TYR cc_start: 0.7242 (OUTLIER) cc_final: 0.6587 (t80) REVERT: D 76 ILE cc_start: 0.7047 (OUTLIER) cc_final: 0.6710 (mp) REVERT: D 120 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7874 (tp40) REVERT: D 203 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.7982 (t70) REVERT: D 374 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7320 (pm20) REVERT: B 75 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7130 (pp) REVERT: B 336 MET cc_start: 0.8898 (ttm) cc_final: 0.8494 (ttm) REVERT: B 369 ASN cc_start: 0.7133 (m110) cc_final: 0.6682 (p0) REVERT: E 70 ASP cc_start: 0.7557 (t0) cc_final: 0.7239 (t0) REVERT: A 49 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7121 (mp) REVERT: C 46 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8402 (mp) REVERT: C 74 GLN cc_start: 0.8254 (pm20) cc_final: 0.7914 (pm20) REVERT: C 203 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8436 (m-30) outliers start: 35 outliers final: 18 residues processed: 175 average time/residue: 1.2911 time to fit residues: 250.5386 Evaluate side-chains 168 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.088569 restraints weight = 22405.833| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.70 r_work: 0.2965 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16095 Z= 0.126 Angle : 0.479 8.149 21924 Z= 0.251 Chirality : 0.037 0.160 2375 Planarity : 0.004 0.052 2756 Dihedral : 5.217 84.841 2089 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.01 % Allowed : 14.40 % Favored : 83.60 % 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: 1.34 (0.19), residues: 1870 helix: 1.55 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.43 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 185 HIS 0.003 0.001 HIS C 178 PHE 0.017 0.001 PHE A 248 TYR 0.031 0.001 TYR C 97 ARG 0.014 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.05103 ( 963) hydrogen bonds : angle 4.19451 ( 2793) covalent geometry : bond 0.00279 (16095) covalent geometry : angle 0.47868 (21924) ********************** 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 181 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.809 Fit side-chains revert: symmetry clash REVERT: D 68 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6513 (t80) REVERT: D 120 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7906 (tp40) REVERT: D 203 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8079 (t70) REVERT: D 374 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7335 (pm20) REVERT: B 75 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7101 (pp) REVERT: B 336 MET cc_start: 0.8886 (ttm) cc_final: 0.8412 (ttm) REVERT: E 70 ASP cc_start: 0.7530 (t0) cc_final: 0.7228 (t0) REVERT: A 49 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7119 (mp) REVERT: C 46 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8324 (mp) REVERT: C 74 GLN cc_start: 0.8196 (pm20) cc_final: 0.7829 (pm20) REVERT: C 371 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7119 (pm20) outliers start: 34 outliers final: 18 residues processed: 175 average time/residue: 1.2929 time to fit residues: 250.1026 Evaluate side-chains 167 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 120 GLN Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 369 ASN Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 371 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 108 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.088968 restraints weight = 22325.320| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.70 r_work: 0.2973 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16095 Z= 0.124 Angle : 0.480 8.164 21924 Z= 0.251 Chirality : 0.037 0.166 2375 Planarity : 0.004 0.053 2756 Dihedral : 5.046 83.943 2087 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.06 % Allowed : 14.57 % Favored : 83.36 % 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: 1.38 (0.19), residues: 1870 helix: 1.58 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.42 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 185 HIS 0.003 0.001 HIS C 178 PHE 0.016 0.001 PHE A 248 TYR 0.029 0.001 TYR C 97 ARG 0.013 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.05062 ( 963) hydrogen bonds : angle 4.17336 ( 2793) covalent geometry : bond 0.00274 (16095) covalent geometry : angle 0.48034 (21924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9660.67 seconds wall clock time: 167 minutes 26.01 seconds (10046.01 seconds total)