Starting phenix.real_space_refine on Thu Sep 18 09:06:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dym_47309/09_2025/9dym_47309.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dym_47309/09_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_47309/09_2025/9dym_47309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dym_47309/09_2025/9dym_47309.map" model { file = "/net/cci-nas-00/data/ceres_data/9dym_47309/09_2025/9dym_47309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dym_47309/09_2025/9dym_47309.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.65, per 1000 atoms: 0.23 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: 1.45 Conformation dependent library (CDL) restraints added in 681.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.41 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: 3.00 Time building geometry restraints manager: 1.80 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 601) selection = (chain 'B' and resid 2 through 601) selection = chain 'C' selection = (chain 'D' and resid 2 through 601) selection = (chain 'E' and resid 2 through 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: 5.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.020 Find NCS groups from input model: 0.360 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:8.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.080 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.043 0.004 ARG A 51 TYR 0.051 0.011 TYR A 44 PHE 0.050 0.010 PHE E 276 TRP 0.055 0.012 TRP E 309 HIS 0.024 0.004 HIS C 168 Details of bonding type rmsd covalent geometry : bond 0.01320 (16095) covalent geometry : angle 1.31340 (21924) hydrogen bonds : bond 0.15000 ( 963) hydrogen bonds : angle 5.36124 ( 2793) *********************** 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 : 0.619 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: 0.6735 time to fit residues: 148.8213 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 : 0.605 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.106141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.087360 restraints weight = 21891.929| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.74 r_work: 0.2940 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1121 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= 0.126 Angle : 0.507 8.456 21924 Z= 0.269 Chirality : 0.038 0.189 2375 Planarity : 0.004 0.039 2756 Dihedral : 6.355 89.126 2107 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.71 % Allowed : 11.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.19), residues: 1870 helix: 1.72 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.19 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 331 TYR 0.019 0.001 TYR E 68 PHE 0.016 0.001 PHE A 248 TRP 0.019 0.001 TRP B 309 HIS 0.003 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00259 (16095) covalent geometry : angle 0.50695 (21924) hydrogen bonds : bond 0.05606 ( 963) hydrogen bonds : angle 4.36312 ( 2793) *********************** 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 205 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.676 Fit side-chains REVERT: D 64 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7323 (mmtm) REVERT: D 68 TYR cc_start: 0.7018 (OUTLIER) cc_final: 0.6266 (t80) REVERT: D 203 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8037 (t70) REVERT: D 374 GLU cc_start: 0.7277 (pm20) cc_final: 0.7004 (pm20) REVERT: B 336 MET cc_start: 0.8827 (ttm) cc_final: 0.8494 (ttm) REVERT: B 365 ASN cc_start: 0.8552 (m110) cc_final: 0.8233 (m-40) REVERT: B 369 ASN cc_start: 0.7080 (m-40) cc_final: 0.6728 (m110) REVERT: E 214 MET cc_start: 0.8029 (tpt) cc_final: 0.6861 (tmm) REVERT: A 49 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7028 (mp) REVERT: C 46 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8346 (mp) REVERT: C 369 ASN cc_start: 0.6783 (m-40) cc_final: 0.6301 (t0) outliers start: 29 outliers final: 9 residues processed: 196 average time/residue: 0.6739 time to fit residues: 145.5339 Evaluate side-chains 168 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 133 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 376 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.084129 restraints weight = 21960.315| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.63 r_work: 0.2888 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16095 Z= 0.238 Angle : 0.574 8.749 21924 Z= 0.303 Chirality : 0.042 0.160 2375 Planarity : 0.005 0.042 2756 Dihedral : 5.732 88.845 2089 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.54 % Allowed : 11.92 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.19), residues: 1870 helix: 1.38 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.48 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 331 TYR 0.033 0.002 TYR C 97 PHE 0.026 0.002 PHE A 248 TRP 0.018 0.002 TRP B 309 HIS 0.007 0.002 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00571 (16095) covalent geometry : angle 0.57390 (21924) hydrogen bonds : bond 0.06403 ( 963) hydrogen bonds : angle 4.41753 ( 2793) *********************** 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 204 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: D 64 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7498 (mmtm) REVERT: D 68 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.6563 (t80) REVERT: D 76 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6662 (mp) REVERT: D 203 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8186 (t70) REVERT: D 333 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8376 (pt0) REVERT: B 75 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7127 (pp) REVERT: B 336 MET cc_start: 0.8952 (ttm) cc_final: 0.8694 (ttp) REVERT: B 369 ASN cc_start: 0.7254 (m-40) cc_final: 0.6904 (m110) REVERT: A 49 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7179 (mp) REVERT: C 46 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8490 (mp) outliers start: 43 outliers final: 14 residues processed: 188 average time/residue: 0.7142 time to fit residues: 147.1946 Evaluate side-chains 167 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 303 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 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 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 152 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 169 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 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 = 0.3302 r_free = 0.3302 target = 0.106093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.087471 restraints weight = 22073.504| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.72 r_work: 0.2942 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1456 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= 0.115 Angle : 0.471 8.186 21924 Z= 0.249 Chirality : 0.037 0.150 2375 Planarity : 0.004 0.042 2756 Dihedral : 5.225 87.875 2087 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.24 % Allowed : 12.92 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.19), residues: 1870 helix: 1.54 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.46 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 331 TYR 0.020 0.001 TYR C 97 PHE 0.016 0.001 PHE A 248 TRP 0.015 0.001 TRP B 309 HIS 0.002 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00239 (16095) covalent geometry : angle 0.47097 (21924) hydrogen bonds : bond 0.05072 ( 963) hydrogen bonds : angle 4.25342 ( 2793) *********************** 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 205 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: D 40 LEU cc_start: 0.7848 (tt) cc_final: 0.7631 (tp) REVERT: D 64 LYS cc_start: 0.8028 (mtmt) cc_final: 0.7400 (mmtm) REVERT: D 68 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.6446 (t80) REVERT: D 76 ILE cc_start: 0.6796 (OUTLIER) cc_final: 0.6520 (mp) REVERT: D 203 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8053 (t70) REVERT: B 75 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7025 (pp) REVERT: B 336 MET cc_start: 0.8878 (ttm) cc_final: 0.8397 (ttm) REVERT: B 369 ASN cc_start: 0.7018 (m-40) cc_final: 0.6699 (m110) REVERT: E 57 GLU cc_start: 0.6430 (pm20) cc_final: 0.5888 (tt0) REVERT: E 70 ASP cc_start: 0.7507 (t0) cc_final: 0.7185 (t0) REVERT: A 49 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7027 (mp) REVERT: C 46 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8352 (mp) outliers start: 38 outliers final: 13 residues processed: 193 average time/residue: 0.6736 time to fit residues: 143.3540 Evaluate side-chains 169 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 249 LEU Chi-restraints excluded: chain D residue 287 TRP 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 122 optimal weight: 0.0870 chunk 138 optimal weight: 1.9990 chunk 175 optimal weight: 0.0020 chunk 119 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 overall best weight: 1.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.105765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.087216 restraints weight = 22319.805| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.68 r_work: 0.2943 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1435 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= 0.159 Angle : 0.503 8.397 21924 Z= 0.264 Chirality : 0.039 0.155 2375 Planarity : 0.004 0.041 2756 Dihedral : 5.227 87.211 2087 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.42 % Allowed : 12.86 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.19), residues: 1870 helix: 1.64 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.29 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 331 TYR 0.031 0.001 TYR C 97 PHE 0.021 0.001 PHE A 248 TRP 0.015 0.001 TRP B 309 HIS 0.005 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00367 (16095) covalent geometry : angle 0.50329 (21924) hydrogen bonds : bond 0.05515 ( 963) hydrogen bonds : angle 4.26264 ( 2793) *********************** 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 196 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: D 68 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.6541 (t80) REVERT: D 76 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6601 (mp) REVERT: D 120 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7843 (tp40) REVERT: D 203 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8120 (t70) REVERT: D 370 LYS cc_start: 0.7816 (tttp) cc_final: 0.7579 (tttp) REVERT: D 374 GLU cc_start: 0.7450 (pm20) cc_final: 0.7139 (pm20) REVERT: B 75 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7105 (pp) REVERT: B 336 MET cc_start: 0.8915 (ttm) cc_final: 0.8455 (ttm) REVERT: E 70 ASP cc_start: 0.7577 (t0) cc_final: 0.7257 (t0) REVERT: E 214 MET cc_start: 0.8160 (tpt) cc_final: 0.7066 (tmm) REVERT: A 49 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7123 (mp) REVERT: C 46 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8476 (mp) REVERT: C 169 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8317 (ttpt) outliers start: 41 outliers final: 17 residues processed: 183 average time/residue: 0.6349 time to fit residues: 128.3571 Evaluate side-chains 172 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 120 GLN Chi-restraints excluded: chain D residue 203 ASP 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 28 ILE 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 129 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 169 LYS 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 0 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3298 r_free = 0.3298 target = 0.105270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.086721 restraints weight = 22280.802| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.68 r_work: 0.2936 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1463 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= 0.169 Angle : 0.511 8.416 21924 Z= 0.268 Chirality : 0.039 0.154 2375 Planarity : 0.004 0.041 2756 Dihedral : 5.241 87.463 2087 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.77 % Allowed : 13.16 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.19), residues: 1870 helix: 1.62 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.33 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 331 TYR 0.026 0.001 TYR C 97 PHE 0.022 0.001 PHE A 248 TRP 0.015 0.001 TRP B 309 HIS 0.005 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00394 (16095) covalent geometry : angle 0.51056 (21924) hydrogen bonds : bond 0.05610 ( 963) hydrogen bonds : angle 4.27076 ( 2793) *********************** 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 200 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: D 61 MET cc_start: 0.5276 (OUTLIER) cc_final: 0.4985 (ptt) REVERT: D 68 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.6454 (t80) REVERT: D 76 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6674 (mp) REVERT: D 203 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8115 (t70) REVERT: D 370 LYS cc_start: 0.7776 (tttp) cc_final: 0.7539 (tttp) REVERT: D 374 GLU cc_start: 0.7545 (pm20) cc_final: 0.7231 (pm20) REVERT: B 75 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7123 (pp) REVERT: B 336 MET cc_start: 0.8919 (ttm) cc_final: 0.8460 (ttm) REVERT: E 70 ASP cc_start: 0.7591 (t0) cc_final: 0.7273 (t0) REVERT: E 214 MET cc_start: 0.8164 (tpt) cc_final: 0.7090 (tmm) REVERT: A 49 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7129 (mp) REVERT: C 46 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8436 (mp) REVERT: C 169 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8337 (ttpt) REVERT: C 371 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7096 (pm20) outliers start: 47 outliers final: 18 residues processed: 185 average time/residue: 0.6267 time to fit residues: 127.9613 Evaluate side-chains 173 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 MET 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 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 169 LYS Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 371 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 106 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.107961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.089595 restraints weight = 22105.244| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.66 r_work: 0.2984 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16095 Z= 0.116 Angle : 0.469 8.095 21924 Z= 0.246 Chirality : 0.037 0.150 2375 Planarity : 0.004 0.041 2756 Dihedral : 5.086 86.179 2087 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.18 % Allowed : 13.86 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.19), residues: 1870 helix: 1.59 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.45 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 331 TYR 0.022 0.001 TYR C 97 PHE 0.015 0.001 PHE A 248 TRP 0.014 0.001 TRP C 309 HIS 0.003 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00250 (16095) covalent geometry : angle 0.46913 (21924) hydrogen bonds : bond 0.04991 ( 963) hydrogen bonds : angle 4.17940 ( 2793) *********************** 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 193 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: D 61 MET cc_start: 0.5223 (OUTLIER) cc_final: 0.4932 (ptt) REVERT: D 68 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6545 (t80) REVERT: D 76 ILE cc_start: 0.7030 (OUTLIER) cc_final: 0.6723 (mp) REVERT: D 203 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8039 (t70) REVERT: D 370 LYS cc_start: 0.7814 (tttp) cc_final: 0.7586 (tttp) REVERT: D 374 GLU cc_start: 0.7563 (pm20) cc_final: 0.7223 (pm20) REVERT: B 75 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7113 (pp) REVERT: B 336 MET cc_start: 0.8891 (ttm) cc_final: 0.8422 (ttm) REVERT: B 369 ASN cc_start: 0.7000 (m110) cc_final: 0.6652 (p0) REVERT: E 70 ASP cc_start: 0.7533 (t0) cc_final: 0.7235 (t0) REVERT: A 49 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7081 (mp) REVERT: C 46 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8447 (mp) REVERT: C 169 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8276 (ttpt) REVERT: C 371 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7111 (pm20) outliers start: 37 outliers final: 15 residues processed: 184 average time/residue: 0.6414 time to fit residues: 129.9307 Evaluate side-chains 168 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 MET 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 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 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 169 LYS Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 371 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 15 optimal weight: 0.0670 chunk 100 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 105 optimal weight: 0.1980 chunk 25 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.109319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.090983 restraints weight = 22130.759| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.67 r_work: 0.3002 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16095 Z= 0.109 Angle : 0.460 8.036 21924 Z= 0.241 Chirality : 0.036 0.150 2375 Planarity : 0.004 0.043 2756 Dihedral : 4.940 84.826 2087 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.30 % Allowed : 14.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.19), residues: 1870 helix: 1.67 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.36 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 331 TYR 0.028 0.001 TYR C 97 PHE 0.013 0.001 PHE A 248 TRP 0.012 0.001 TRP B 309 HIS 0.002 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00231 (16095) covalent geometry : angle 0.45997 (21924) hydrogen bonds : bond 0.04805 ( 963) hydrogen bonds : angle 4.12655 ( 2793) *********************** 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 190 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: D 68 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6473 (t80) REVERT: D 76 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6664 (mp) REVERT: D 120 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7816 (tp40) REVERT: D 203 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.7952 (t70) REVERT: D 324 GLU cc_start: 0.8146 (mp0) cc_final: 0.7769 (mp0) REVERT: D 374 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7226 (pm20) REVERT: B 75 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7119 (pp) REVERT: B 336 MET cc_start: 0.8866 (ttm) cc_final: 0.8432 (ttm) REVERT: B 369 ASN cc_start: 0.7152 (m110) cc_final: 0.6707 (p0) REVERT: E 70 ASP cc_start: 0.7325 (t0) cc_final: 0.7112 (t0) REVERT: E 74 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7585 (pm20) REVERT: A 49 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7110 (mp) REVERT: C 46 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8327 (mp) REVERT: C 169 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8262 (ttpt) REVERT: C 203 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8328 (m-30) REVERT: C 371 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7137 (pm20) outliers start: 39 outliers final: 15 residues processed: 181 average time/residue: 0.6442 time to fit residues: 128.9832 Evaluate side-chains 166 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 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 369 ASN Chi-restraints excluded: chain A residue 49 ILE 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 169 LYS Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 235 VAL 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 51 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.106702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.088169 restraints weight = 22261.742| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.68 r_work: 0.2958 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1653 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= 0.150 Angle : 0.495 8.265 21924 Z= 0.260 Chirality : 0.038 0.152 2375 Planarity : 0.004 0.048 2756 Dihedral : 5.010 84.159 2087 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.24 % Allowed : 14.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.000 ARG C 331 TYR 0.030 0.001 TYR C 97 PHE 0.020 0.001 PHE B 248 TRP 0.015 0.001 TRP C 309 HIS 0.004 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00346 (16095) covalent geometry : angle 0.49515 (21924) hydrogen bonds : bond 0.05330 ( 963) hydrogen bonds : angle 4.18091 ( 2793) *********************** 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 186 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: D 68 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.6551 (t80) REVERT: D 76 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6723 (mp) REVERT: D 120 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7869 (tp40) REVERT: D 203 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8072 (t70) REVERT: D 370 LYS cc_start: 0.7800 (tttp) cc_final: 0.7560 (tttp) REVERT: D 374 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: B 75 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7130 (pp) REVERT: B 336 MET cc_start: 0.8899 (ttm) cc_final: 0.8437 (ttm) REVERT: B 369 ASN cc_start: 0.7046 (m110) cc_final: 0.6599 (p0) REVERT: E 70 ASP cc_start: 0.7353 (t0) cc_final: 0.7125 (t0) REVERT: E 214 MET cc_start: 0.8149 (tpt) cc_final: 0.7055 (tmm) REVERT: A 49 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7088 (mp) REVERT: C 46 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8431 (mp) REVERT: C 169 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8289 (ttpt) REVERT: C 371 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7094 (pm20) outliers start: 38 outliers final: 18 residues processed: 176 average time/residue: 0.6646 time to fit residues: 129.0230 Evaluate side-chains 171 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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 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 129 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 169 LYS 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 74 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3292 r_free = 0.3292 target = 0.104849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.086188 restraints weight = 22313.988| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.69 r_work: 0.2926 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16095 Z= 0.187 Angle : 0.528 8.424 21924 Z= 0.277 Chirality : 0.040 0.153 2375 Planarity : 0.004 0.053 2756 Dihedral : 4.994 85.427 2085 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.95 % Allowed : 14.57 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.19), residues: 1870 helix: 1.64 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.27 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 331 TYR 0.032 0.002 TYR C 97 PHE 0.024 0.002 PHE A 248 TRP 0.017 0.002 TRP D 185 HIS 0.005 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00441 (16095) covalent geometry : angle 0.52830 (21924) hydrogen bonds : bond 0.05733 ( 963) hydrogen bonds : angle 4.26665 ( 2793) ********************** 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 177 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: D 68 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6579 (t80) REVERT: D 76 ILE cc_start: 0.7102 (OUTLIER) cc_final: 0.6759 (mp) REVERT: D 120 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7862 (tp40) REVERT: D 203 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8139 (t70) REVERT: D 374 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: B 75 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7150 (pp) REVERT: B 336 MET cc_start: 0.8893 (ttm) cc_final: 0.8408 (ttm) REVERT: B 369 ASN cc_start: 0.7156 (m110) cc_final: 0.6497 (p0) REVERT: E 70 ASP cc_start: 0.7347 (t0) cc_final: 0.7068 (t0) REVERT: E 214 MET cc_start: 0.8112 (tpt) cc_final: 0.7022 (tmm) REVERT: A 49 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7087 (mp) REVERT: C 46 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8370 (mp) REVERT: C 169 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8288 (ttpt) REVERT: C 371 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7040 (pm20) outliers start: 33 outliers final: 19 residues processed: 170 average time/residue: 0.6664 time to fit residues: 125.2534 Evaluate side-chains 168 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 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 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 129 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 169 LYS 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 162 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 145 optimal weight: 0.0770 chunk 157 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.105397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.086789 restraints weight = 22230.038| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.69 r_work: 0.2940 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16095 Z= 0.157 Angle : 0.507 8.311 21924 Z= 0.266 Chirality : 0.039 0.184 2375 Planarity : 0.004 0.053 2756 Dihedral : 4.975 85.755 2085 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.12 % Allowed : 14.45 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.19), residues: 1870 helix: 1.63 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.29 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 331 TYR 0.031 0.001 TYR C 97 PHE 0.021 0.001 PHE A 248 TRP 0.017 0.001 TRP D 185 HIS 0.005 0.001 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00363 (16095) covalent geometry : angle 0.50666 (21924) hydrogen bonds : bond 0.05483 ( 963) hydrogen bonds : angle 4.24790 ( 2793) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4706.85 seconds wall clock time: 81 minutes 16.06 seconds (4876.06 seconds total)