Starting phenix.real_space_refine on Sat Jun 14 00:15:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dym_47309/06_2025/9dym_47309.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dym_47309/06_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_47309/06_2025/9dym_47309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dym_47309/06_2025/9dym_47309.map" model { file = "/net/cci-nas-00/data/ceres_data/9dym_47309/06_2025/9dym_47309.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dym_47309/06_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-5710/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: 10.41, per 1000 atoms: 0.67 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: 4.35 Conformation dependent library (CDL) restraints added in 2.1 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: 1.61 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: 4.54 Time building geometry restraints manager: 5.07 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.820 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 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:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.460 ------------------------------------------------------------------------------- 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 : 1.759 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: 1.3742 time to fit residues: 305.6680 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 : 1.838 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.086928 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: 0.8424 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 : 1.722 Fit side-chains REVERT: D 64 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7298 (mmtm) REVERT: D 68 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.6232 (t80) REVERT: D 203 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8057 (t70) REVERT: B 336 MET cc_start: 0.8877 (ttm) cc_final: 0.8495 (ttm) REVERT: B 365 ASN cc_start: 0.8555 (m110) cc_final: 0.8238 (m-40) REVERT: B 369 ASN cc_start: 0.7099 (m-40) cc_final: 0.6764 (m110) REVERT: E 214 MET cc_start: 0.8031 (tpt) cc_final: 0.6874 (tmm) REVERT: A 49 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7028 (mp) REVERT: C 46 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8329 (mp) REVERT: C 369 ASN cc_start: 0.6834 (m-40) cc_final: 0.6332 (t0) outliers start: 32 outliers final: 9 residues processed: 193 average time/residue: 1.4076 time to fit residues: 300.1056 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 : 1.693 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.0870 chunk 101 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.106114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.087374 restraints weight = 21829.423| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.72 r_work: 0.2929 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16095 Z= 0.126 Angle : 0.481 8.322 21924 Z= 0.253 Chirality : 0.037 0.152 2375 Planarity : 0.004 0.040 2756 Dihedral : 5.474 89.754 2089 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.24 % Allowed : 11.92 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.60 (0.19), residues: 1870 helix: 1.74 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.20 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 309 HIS 0.003 0.001 HIS C 178 PHE 0.018 0.001 PHE A 248 TYR 0.027 0.001 TYR C 97 ARG 0.007 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.05275 ( 963) hydrogen bonds : angle 4.24665 ( 2793) covalent geometry : bond 0.00271 (16095) covalent geometry : angle 0.48081 (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 204 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 1.678 Fit side-chains revert: symmetry clash REVERT: D 61 MET cc_start: 0.5305 (ptt) cc_final: 0.5104 (ptt) REVERT: D 64 LYS cc_start: 0.8035 (mtmt) cc_final: 0.7383 (mmtm) REVERT: D 68 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.6369 (t80) REVERT: D 76 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6469 (mp) REVERT: D 203 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8099 (t70) REVERT: D 333 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8234 (pt0) REVERT: D 374 GLU cc_start: 0.7344 (pm20) cc_final: 0.6946 (pm20) REVERT: B 75 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6972 (pp) REVERT: B 336 MET cc_start: 0.8863 (ttm) cc_final: 0.8381 (ttm) REVERT: B 369 ASN cc_start: 0.7191 (m-40) cc_final: 0.6830 (m110) REVERT: A 49 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7060 (mp) REVERT: C 46 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8338 (mp) outliers start: 38 outliers final: 13 residues processed: 191 average time/residue: 1.4261 time to fit residues: 301.3399 Evaluate side-chains 166 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.857 ------------------------------------------------------------------------------- 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: 7.9990 chunk 2 optimal weight: 0.0980 chunk 144 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.104069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.085271 restraints weight = 21910.254| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.71 r_work: 0.2908 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16095 Z= 0.157 Angle : 0.505 8.411 21924 Z= 0.266 Chirality : 0.039 0.155 2375 Planarity : 0.004 0.041 2756 Dihedral : 5.449 87.429 2089 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.42 % Allowed : 12.68 % 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: 1.54 (0.19), residues: 1870 helix: 1.69 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.22 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 309 HIS 0.005 0.001 HIS C 178 PHE 0.021 0.001 PHE A 248 TYR 0.030 0.001 TYR C 97 ARG 0.007 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.05585 ( 963) hydrogen bonds : angle 4.25732 ( 2793) covalent geometry : bond 0.00359 (16095) covalent geometry : angle 0.50490 (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 200 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 2.020 Fit side-chains REVERT: D 68 TYR cc_start: 0.7167 (OUTLIER) cc_final: 0.6477 (t80) REVERT: D 76 ILE cc_start: 0.6820 (OUTLIER) cc_final: 0.6511 (mp) REVERT: D 203 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8125 (t70) REVERT: D 333 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8268 (pt0) REVERT: D 374 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7274 (pm20) REVERT: B 75 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7044 (pp) REVERT: B 336 MET cc_start: 0.8876 (ttm) cc_final: 0.8412 (ttm) REVERT: B 369 ASN cc_start: 0.7220 (m-40) cc_final: 0.6814 (m110) REVERT: E 57 GLU cc_start: 0.6401 (pm20) cc_final: 0.5680 (tt0) REVERT: E 70 ASP cc_start: 0.7495 (t0) cc_final: 0.7165 (t0) REVERT: E 117 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.7895 (mmtt) REVERT: E 214 MET cc_start: 0.8102 (tpt) cc_final: 0.6983 (tmm) REVERT: A 49 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7080 (mp) REVERT: C 46 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8346 (mp) REVERT: C 369 ASN cc_start: 0.6821 (m-40) cc_final: 0.6283 (t0) outliers start: 41 outliers final: 16 residues processed: 189 average time/residue: 1.4115 time to fit residues: 295.3459 Evaluate side-chains 173 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.939 ------------------------------------------------------------------------------- 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 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 117 LYS 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 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: 0.9980 chunk 24 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3280 r_free = 0.3280 target = 0.104331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.085545 restraints weight = 22215.873| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.72 r_work: 0.2911 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16095 Z= 0.151 Angle : 0.495 8.380 21924 Z= 0.260 Chirality : 0.038 0.153 2375 Planarity : 0.004 0.041 2756 Dihedral : 5.409 87.269 2089 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.60 % Allowed : 13.16 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.19), residues: 1870 helix: 1.55 (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 0.015 0.001 TRP B 309 HIS 0.004 0.001 HIS C 178 PHE 0.020 0.001 PHE A 248 TYR 0.024 0.001 TYR C 97 ARG 0.009 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.05452 ( 963) hydrogen bonds : angle 4.23501 ( 2793) covalent geometry : bond 0.00346 (16095) covalent geometry : angle 0.49481 (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 202 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 1.756 Fit side-chains REVERT: D 68 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.6439 (t80) REVERT: D 76 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6527 (mp) REVERT: D 120 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7778 (tp40) REVERT: D 203 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8135 (t70) REVERT: D 333 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8238 (pt0) REVERT: D 374 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7249 (pm20) REVERT: B 75 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7030 (pp) REVERT: B 336 MET cc_start: 0.8882 (ttm) cc_final: 0.8475 (ttm) REVERT: B 369 ASN cc_start: 0.7066 (m-40) cc_final: 0.6736 (m110) REVERT: E 70 ASP cc_start: 0.7527 (t0) cc_final: 0.7208 (t0) REVERT: E 214 MET cc_start: 0.8081 (tpt) cc_final: 0.6954 (tmm) REVERT: A 49 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7059 (mp) REVERT: C 46 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8354 (mp) REVERT: C 74 GLN cc_start: 0.8236 (mp10) cc_final: 0.7641 (pm20) REVERT: C 369 ASN cc_start: 0.6780 (m-40) cc_final: 0.6268 (t0) outliers start: 44 outliers final: 20 residues processed: 190 average time/residue: 1.3466 time to fit residues: 283.3403 Evaluate side-chains 172 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.852 ------------------------------------------------------------------------------- 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 303 ASP 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 67 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 184 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.5364 ------------------------------------------------------------------------------- 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 = 0.3271 r_free = 0.3271 target = 0.103702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.084861 restraints weight = 22069.668| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.72 r_work: 0.2891 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1438 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= 0.169 Angle : 0.512 8.437 21924 Z= 0.269 Chirality : 0.039 0.154 2375 Planarity : 0.004 0.042 2756 Dihedral : 5.424 87.021 2089 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.60 % Allowed : 13.27 % Favored : 84.13 % 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: 1.30 (0.19), residues: 1870 helix: 1.52 (0.14), residues: 1255 sheet: None (None), residues: 0 loop : -0.45 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 309 HIS 0.005 0.001 HIS C 178 PHE 0.022 0.001 PHE A 248 TYR 0.031 0.001 TYR C 97 ARG 0.010 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.05601 ( 963) hydrogen bonds : angle 4.25531 ( 2793) covalent geometry : bond 0.00393 (16095) covalent geometry : angle 0.51158 (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 192 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 1.666 Fit side-chains REVERT: D 68 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6518 (t80) REVERT: D 76 ILE cc_start: 0.6956 (OUTLIER) cc_final: 0.6632 (mp) REVERT: D 120 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7785 (tp40) REVERT: D 203 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8121 (t70) REVERT: D 333 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8268 (pt0) REVERT: D 374 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7279 (pm20) REVERT: B 75 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7043 (pp) REVERT: B 336 MET cc_start: 0.8887 (ttm) cc_final: 0.8411 (ttm) REVERT: B 369 ASN cc_start: 0.7079 (m-40) cc_final: 0.6872 (m110) REVERT: E 70 ASP cc_start: 0.7571 (t0) cc_final: 0.7248 (t0) REVERT: E 74 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7644 (pp30) REVERT: E 214 MET cc_start: 0.8105 (tpt) cc_final: 0.6995 (tmm) REVERT: A 49 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7065 (mp) REVERT: C 46 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8329 (mp) REVERT: C 74 GLN cc_start: 0.8236 (mp10) cc_final: 0.7611 (pm20) REVERT: C 369 ASN cc_start: 0.6767 (m-40) cc_final: 0.6206 (t0) outliers start: 44 outliers final: 20 residues processed: 180 average time/residue: 1.2264 time to fit residues: 245.7157 Evaluate side-chains 175 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 1.877 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 54 optimal weight: 0.0770 chunk 175 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 134 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.107915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.089479 restraints weight = 22112.735| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.67 r_work: 0.2989 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16095 Z= 0.111 Angle : 0.466 8.109 21924 Z= 0.245 Chirality : 0.036 0.150 2375 Planarity : 0.004 0.042 2756 Dihedral : 5.237 85.601 2089 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.42 % Allowed : 13.81 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.45 (0.19), residues: 1870 helix: 1.63 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.41 (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 0.024 0.001 TYR C 97 ARG 0.012 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.04940 ( 963) hydrogen bonds : angle 4.16068 ( 2793) covalent geometry : bond 0.00232 (16095) covalent geometry : angle 0.46627 (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 204 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 1.828 Fit side-chains revert: symmetry clash REVERT: D 68 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.6567 (t80) REVERT: D 76 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6728 (mp) REVERT: D 120 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7863 (tp40) REVERT: D 203 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8075 (t70) REVERT: D 374 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7221 (pm20) REVERT: B 75 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7129 (pp) REVERT: B 336 MET cc_start: 0.8896 (ttm) cc_final: 0.8438 (ttm) REVERT: B 369 ASN cc_start: 0.7159 (m-40) cc_final: 0.6930 (m110) REVERT: E 70 ASP cc_start: 0.7560 (t0) cc_final: 0.7246 (t0) REVERT: A 49 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7103 (mp) REVERT: C 46 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8412 (mp) REVERT: C 74 GLN cc_start: 0.8232 (mp10) cc_final: 0.7644 (pm20) outliers start: 41 outliers final: 18 residues processed: 192 average time/residue: 1.6438 time to fit residues: 350.5601 Evaluate side-chains 176 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 3.611 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 63 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3228 r_free = 0.3228 target = 0.101191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.082041 restraints weight = 21894.628| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.65 r_work: 0.2847 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 16095 Z= 0.315 Angle : 0.621 9.005 21924 Z= 0.326 Chirality : 0.045 0.160 2375 Planarity : 0.005 0.042 2756 Dihedral : 5.654 88.378 2089 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.24 % Allowed : 13.98 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.96 (0.19), residues: 1870 helix: 1.26 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.57 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 309 HIS 0.008 0.002 HIS C 178 PHE 0.032 0.002 PHE A 248 TYR 0.040 0.002 TYR C 97 ARG 0.010 0.001 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.06787 ( 963) hydrogen bonds : angle 4.44765 ( 2793) covalent geometry : bond 0.00767 (16095) covalent geometry : angle 0.62099 (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 184 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 1.767 Fit side-chains REVERT: D 68 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6693 (t80) REVERT: D 76 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6787 (mp) REVERT: D 203 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8099 (t70) REVERT: D 374 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: B 75 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7086 (pp) REVERT: B 336 MET cc_start: 0.8973 (ttm) cc_final: 0.8737 (ttp) REVERT: E 70 ASP cc_start: 0.7619 (t0) cc_final: 0.7286 (t0) REVERT: E 374 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: A 49 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7106 (mp) REVERT: C 46 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8377 (mp) REVERT: C 369 ASN cc_start: 0.6866 (m-40) cc_final: 0.6284 (t0) REVERT: C 371 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6809 (pm20) outliers start: 38 outliers final: 15 residues processed: 176 average time/residue: 1.5181 time to fit residues: 296.2081 Evaluate side-chains 164 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.880 ------------------------------------------------------------------------------- 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 203 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 205 ILE 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 E residue 374 GLU 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 371 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 124 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.105408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.086841 restraints weight = 22265.008| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.69 r_work: 0.2938 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1533 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= 0.143 Angle : 0.501 8.301 21924 Z= 0.264 Chirality : 0.038 0.153 2375 Planarity : 0.004 0.045 2756 Dihedral : 5.416 87.346 2089 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.95 % Allowed : 14.40 % 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: 1.32 (0.19), residues: 1870 helix: 1.54 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.36 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 309 HIS 0.004 0.001 HIS C 178 PHE 0.020 0.001 PHE A 248 TYR 0.031 0.001 TYR C 97 ARG 0.012 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.05428 ( 963) hydrogen bonds : angle 4.28849 ( 2793) covalent geometry : bond 0.00324 (16095) covalent geometry : angle 0.50088 (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 181 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 1.921 Fit side-chains revert: symmetry clash REVERT: D 68 TYR cc_start: 0.7253 (OUTLIER) cc_final: 0.6551 (t80) REVERT: D 76 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6718 (mp) REVERT: D 203 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8090 (t70) REVERT: D 374 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7320 (pm20) REVERT: B 75 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7132 (pp) REVERT: B 336 MET cc_start: 0.8924 (ttm) cc_final: 0.8489 (ttm) REVERT: E 70 ASP cc_start: 0.7580 (t0) cc_final: 0.7251 (t0) REVERT: E 214 MET cc_start: 0.8078 (tpt) cc_final: 0.6972 (tmm) REVERT: A 49 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7112 (mp) REVERT: C 46 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8403 (mp) REVERT: C 203 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8424 (m-30) REVERT: C 371 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7063 (pm20) outliers start: 33 outliers final: 17 residues processed: 175 average time/residue: 1.4329 time to fit residues: 277.3569 Evaluate side-chains 168 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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 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 205 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 129 ILE 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 371 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3305 r_free = 0.3305 target = 0.105748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.087101 restraints weight = 22431.265| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.70 r_work: 0.2943 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16095 Z= 0.145 Angle : 0.495 8.285 21924 Z= 0.261 Chirality : 0.038 0.154 2375 Planarity : 0.004 0.052 2756 Dihedral : 5.321 85.947 2089 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.71 % Allowed : 14.40 % Favored : 83.89 % 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: 1.23 (0.19), residues: 1870 helix: 1.49 (0.14), residues: 1255 sheet: None (None), residues: 0 loop : -0.50 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 185 HIS 0.004 0.001 HIS C 178 PHE 0.020 0.001 PHE A 248 TYR 0.030 0.001 TYR C 97 ARG 0.013 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.05358 ( 963) hydrogen bonds : angle 4.24793 ( 2793) covalent geometry : bond 0.00329 (16095) covalent geometry : angle 0.49508 (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 172 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 1.934 Fit side-chains revert: symmetry clash REVERT: D 68 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.6550 (t80) REVERT: D 76 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6762 (mp) REVERT: D 120 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7865 (tp40) REVERT: D 203 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8069 (t70) REVERT: D 374 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7324 (pm20) REVERT: B 75 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7120 (pp) REVERT: B 336 MET cc_start: 0.8911 (ttm) cc_final: 0.8511 (ttm) REVERT: E 70 ASP cc_start: 0.7552 (t0) cc_final: 0.7241 (t0) REVERT: E 214 MET cc_start: 0.8110 (tpt) cc_final: 0.7016 (tmm) REVERT: A 49 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7122 (mp) REVERT: C 46 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8335 (mp) REVERT: C 371 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7060 (pm20) outliers start: 29 outliers final: 15 residues processed: 165 average time/residue: 1.5042 time to fit residues: 274.2890 Evaluate side-chains 160 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 2.097 ------------------------------------------------------------------------------- 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 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 205 ILE 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 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: 2.9990 chunk 104 optimal weight: 3.9990 chunk 109 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 140 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.107251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.088674 restraints weight = 22358.751| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.70 r_work: 0.2966 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1671 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 8.496 21924 Z= 0.252 Chirality : 0.037 0.161 2375 Planarity : 0.004 0.053 2756 Dihedral : 5.104 84.972 2087 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.89 % Allowed : 14.34 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.31 (0.19), residues: 1870 helix: 1.54 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.47 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 185 HIS 0.003 0.001 HIS C 178 PHE 0.017 0.001 PHE A 248 TYR 0.028 0.001 TYR C 97 ARG 0.014 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.05085 ( 963) hydrogen bonds : angle 4.20168 ( 2793) covalent geometry : bond 0.00274 (16095) covalent geometry : angle 0.48029 (21924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10646.64 seconds wall clock time: 188 minutes 39.23 seconds (11319.23 seconds total)