Starting phenix.real_space_refine on Tue Feb 11 05:37:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5vrf_8728/02_2025/5vrf_8728.cif Found real_map, /net/cci-nas-00/data/ceres_data/5vrf_8728/02_2025/5vrf_8728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5vrf_8728/02_2025/5vrf_8728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5vrf_8728/02_2025/5vrf_8728.map" model { file = "/net/cci-nas-00/data/ceres_data/5vrf_8728/02_2025/5vrf_8728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5vrf_8728/02_2025/5vrf_8728.cif" } resolution = 4.1 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= 0.001 sd= 0.004 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: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 6 5.16 5 C 2828 2.51 5 N 736 2.21 5 O 800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4378 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2185 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain: "A" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2185 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.10, per 1000 atoms: 0.71 Number of scatterers: 4378 At special positions: 0 Unit cell: (102.72, 93.09, 93.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 6 16.00 O 800 8.00 N 736 7.00 C 2828 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: 1.12 Conformation dependent library (CDL) restraints added in 545.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 155 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" ND1 HIS A 73 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 77 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS B 263 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 285 " pdb=" ZN A 304 " pdb="ZN ZN A 304 " - pdb=" NE2 HIS A 234 " pdb="ZN ZN A 304 " - pdb=" ND1 HIS A 250 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 155 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 77 " pdb="ZN ZN B 302 " - pdb=" ND1 HIS B 73 " pdb=" ZN B 303 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS A 263 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS B 285 " pdb=" ZN B 304 " pdb="ZN ZN B 304 " - pdb=" NE2 HIS B 234 " pdb="ZN ZN B 304 " - pdb=" ND1 HIS B 250 " 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1068 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 73.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'B' and resid 9 through 37 removed outlier: 3.677A pdb=" N LEU B 13 " --> pdb=" O PHE B 9 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 66 removed outlier: 3.659A pdb=" N ASP B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 109 removed outlier: 3.880A pdb=" N LEU B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU B 98 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 142 removed outlier: 4.469A pdb=" N VAL B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N SER B 123 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 142 " --> pdb=" O LYS B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 174 removed outlier: 3.882A pdb=" N SER B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 208 removed outlier: 4.047A pdb=" N GLY B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL B 186 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 226 removed outlier: 3.816A pdb=" N GLU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 277 Processing helix chain 'A' and resid 9 through 37 removed outlier: 3.678A pdb=" N LEU A 13 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 66 removed outlier: 3.658A pdb=" N ASP A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 109 removed outlier: 3.880A pdb=" N LEU A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 removed outlier: 4.469A pdb=" N VAL A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER A 123 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 174 removed outlier: 3.881A pdb=" N SER A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 208 removed outlier: 4.047A pdb=" N GLY A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN A 205 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 226 removed outlier: 3.817A pdb=" N GLU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 277 Processing sheet with id=AA1, first strand: chain 'B' and resid 232 through 241 removed outlier: 5.933A pdb=" N LEU B 233 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP B 235 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL B 245 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ILE B 283 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 247 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N HIS B 285 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE B 249 " --> pdb=" O HIS B 285 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASP B 287 " --> pdb=" O PHE B 249 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU B 251 " --> pdb=" O ASP B 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 241 removed outlier: 5.933A pdb=" N LEU A 233 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLU A 252 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP A 235 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL A 245 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N ILE A 283 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A 247 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N HIS A 285 " --> pdb=" O ILE A 247 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE A 249 " --> pdb=" O HIS A 285 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP A 287 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU A 251 " --> pdb=" O ASP A 287 " (cutoff:3.500A) 318 hydrogen bonds defined for protein. 948 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: 1.11 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1251 1.33 - 1.45: 742 1.45 - 1.57: 2455 1.57 - 1.68: 0 1.68 - 1.80: 10 Bond restraints: 4458 Sorted by residual: bond pdb=" CZ TYR B 75 " pdb=" OH TYR B 75 " ideal model delta sigma weight residual 1.376 1.264 0.112 2.10e-02 2.27e+03 2.86e+01 bond pdb=" CZ TYR A 75 " pdb=" OH TYR A 75 " ideal model delta sigma weight residual 1.376 1.264 0.112 2.10e-02 2.27e+03 2.85e+01 bond pdb=" CD1 TYR A 75 " pdb=" CE1 TYR A 75 " ideal model delta sigma weight residual 1.382 1.244 0.138 3.00e-02 1.11e+03 2.12e+01 bond pdb=" CD1 TYR B 75 " pdb=" CE1 TYR B 75 " ideal model delta sigma weight residual 1.382 1.245 0.137 3.00e-02 1.11e+03 2.10e+01 bond pdb=" CD2 TYR B 75 " pdb=" CE2 TYR B 75 " ideal model delta sigma weight residual 1.382 1.256 0.126 3.00e-02 1.11e+03 1.78e+01 ... (remaining 4453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 5614 2.04 - 4.09: 323 4.09 - 6.13: 94 6.13 - 8.17: 35 8.17 - 10.22: 8 Bond angle restraints: 6074 Sorted by residual: angle pdb=" NE ARG B 239 " pdb=" CZ ARG B 239 " pdb=" NH1 ARG B 239 " ideal model delta sigma weight residual 121.50 114.36 7.14 1.00e+00 1.00e+00 5.09e+01 angle pdb=" NE ARG A 239 " pdb=" CZ ARG A 239 " pdb=" NH1 ARG A 239 " ideal model delta sigma weight residual 121.50 114.40 7.10 1.00e+00 1.00e+00 5.05e+01 angle pdb=" NE ARG B 239 " pdb=" CZ ARG B 239 " pdb=" NH2 ARG B 239 " ideal model delta sigma weight residual 119.20 124.11 -4.91 9.00e-01 1.23e+00 2.97e+01 angle pdb=" NE ARG A 239 " pdb=" CZ ARG A 239 " pdb=" NH2 ARG A 239 " ideal model delta sigma weight residual 119.20 124.08 -4.88 9.00e-01 1.23e+00 2.94e+01 angle pdb=" NE ARG B 74 " pdb=" CZ ARG B 74 " pdb=" NH2 ARG B 74 " ideal model delta sigma weight residual 119.20 122.74 -3.54 9.00e-01 1.23e+00 1.54e+01 ... (remaining 6069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.46: 2475 14.46 - 28.91: 99 28.91 - 43.37: 46 43.37 - 57.82: 0 57.82 - 72.28: 2 Dihedral angle restraints: 2622 sinusoidal: 974 harmonic: 1648 Sorted by residual: dihedral pdb=" CA PHE B 246 " pdb=" C PHE B 246 " pdb=" N ILE B 247 " pdb=" CA ILE B 247 " ideal model delta harmonic sigma weight residual -180.00 -157.31 -22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PHE A 246 " pdb=" C PHE A 246 " pdb=" N ILE A 247 " pdb=" CA ILE A 247 " ideal model delta harmonic sigma weight residual 180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA SER A 203 " pdb=" C SER A 203 " pdb=" N ILE A 204 " pdb=" CA ILE A 204 " ideal model delta harmonic sigma weight residual -180.00 -162.03 -17.97 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 2619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 434 0.040 - 0.079: 188 0.079 - 0.119: 78 0.119 - 0.159: 21 0.159 - 0.198: 9 Chirality restraints: 730 Sorted by residual: chirality pdb=" CA GLU A 81 " pdb=" N GLU A 81 " pdb=" C GLU A 81 " pdb=" CB GLU A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.83e-01 chirality pdb=" CA GLU B 81 " pdb=" N GLU B 81 " pdb=" C GLU B 81 " pdb=" CB GLU B 81 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" CB ILE A 283 " pdb=" CA ILE A 283 " pdb=" CG1 ILE A 283 " pdb=" CG2 ILE A 283 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.23e-01 ... (remaining 727 not shown) Planarity restraints: 760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 75 " 0.039 2.00e-02 2.50e+03 2.21e-02 9.75e+00 pdb=" CG TYR A 75 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 75 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 75 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR A 75 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 75 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 75 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR A 75 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 75 " -0.039 2.00e-02 2.50e+03 2.19e-02 9.58e+00 pdb=" CG TYR B 75 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR B 75 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 75 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR B 75 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 75 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 75 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR B 75 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 132 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C ALA B 132 " -0.048 2.00e-02 2.50e+03 pdb=" O ALA B 132 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU B 133 " 0.016 2.00e-02 2.50e+03 ... (remaining 757 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 60 2.58 - 3.16: 3713 3.16 - 3.74: 6983 3.74 - 4.32: 8899 4.32 - 4.90: 14028 Nonbonded interactions: 33683 Sorted by model distance: nonbonded pdb=" OD2 ASP A 287 " pdb="ZN ZN A 304 " model vdw 1.994 2.230 nonbonded pdb=" OD2 ASP B 287 " pdb="ZN ZN B 304 " model vdw 2.020 2.230 nonbonded pdb=" OD2 ASP A 47 " pdb="ZN ZN A 301 " model vdw 2.050 2.230 nonbonded pdb=" OD1 ASP B 287 " pdb="ZN ZN B 303 " model vdw 2.053 2.230 nonbonded pdb=" OD2 ASP B 47 " pdb="ZN ZN B 301 " model vdw 2.067 2.230 ... (remaining 33678 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 0.090 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.130 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.011 0.138 4458 Z= 0.760 Angle : 1.277 10.217 6074 Z= 0.650 Chirality : 0.056 0.198 730 Planarity : 0.008 0.058 760 Dihedral : 10.376 72.280 1554 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.25), residues: 560 helix: -2.45 (0.18), residues: 376 sheet: -0.79 (0.68), residues: 50 loop : -3.64 (0.37), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 33 HIS 0.013 0.003 HIS B 234 PHE 0.032 0.005 PHE B 97 TYR 0.039 0.006 TYR A 75 ARG 0.008 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8382 (tp30) REVERT: B 194 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8355 (tm-30) REVERT: B 198 ASP cc_start: 0.8854 (t0) cc_final: 0.8515 (t0) REVERT: A 81 GLU cc_start: 0.9060 (pp20) cc_final: 0.8507 (pp20) REVERT: A 105 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8321 (tm-30) REVERT: A 198 ASP cc_start: 0.8769 (t0) cc_final: 0.8389 (t0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2654 time to fit residues: 53.6018 Evaluate side-chains 90 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 20.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 HIS B 115 ASN ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN A 71 HIS A 115 ASN A 195 GLN A 205 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.095152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.067519 restraints weight = 12057.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.069258 restraints weight = 7067.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.070420 restraints weight = 4990.731| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4458 Z= 0.265 Angle : 0.648 7.140 6074 Z= 0.340 Chirality : 0.038 0.177 730 Planarity : 0.005 0.045 760 Dihedral : 4.535 15.845 606 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.91 (0.32), residues: 560 helix: 0.25 (0.23), residues: 394 sheet: -0.97 (0.60), residues: 50 loop : -3.18 (0.49), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 177 HIS 0.004 0.001 HIS B 234 PHE 0.016 0.002 PHE A 249 TYR 0.029 0.002 TYR A 175 ARG 0.006 0.001 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 ARG cc_start: 0.8780 (ttp80) cc_final: 0.8518 (ttp80) REVERT: B 24 THR cc_start: 0.9278 (p) cc_final: 0.8999 (p) REVERT: B 27 THR cc_start: 0.9523 (m) cc_final: 0.9287 (p) REVERT: B 105 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8173 (tm-30) REVERT: B 170 LEU cc_start: 0.9464 (tt) cc_final: 0.9244 (tp) REVERT: B 198 ASP cc_start: 0.8927 (t0) cc_final: 0.8526 (t0) REVERT: A 81 GLU cc_start: 0.9152 (pp20) cc_final: 0.8933 (pp20) REVERT: A 105 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8324 (tm-30) REVERT: A 163 ASN cc_start: 0.9225 (t0) cc_final: 0.8747 (t0) REVERT: A 198 ASP cc_start: 0.9003 (t0) cc_final: 0.8739 (t0) REVERT: A 218 GLN cc_start: 0.8200 (tp-100) cc_final: 0.7783 (tm-30) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1953 time to fit residues: 32.2273 Evaluate side-chains 100 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.0070 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 HIS ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN A 234 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.098380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.068452 restraints weight = 12148.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.070257 restraints weight = 7079.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.071413 restraints weight = 4986.727| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4458 Z= 0.158 Angle : 0.576 7.103 6074 Z= 0.284 Chirality : 0.036 0.166 730 Planarity : 0.003 0.034 760 Dihedral : 4.140 14.374 606 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.22 % Allowed : 3.73 % Favored : 96.05 % 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: 0.57 (0.34), residues: 560 helix: 1.45 (0.25), residues: 388 sheet: -0.10 (0.65), residues: 50 loop : -3.01 (0.48), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 177 HIS 0.008 0.001 HIS A 73 PHE 0.010 0.001 PHE A 249 TYR 0.007 0.001 TYR A 175 ARG 0.006 0.001 ARG B 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 LEU cc_start: 0.9390 (tt) cc_final: 0.9007 (tp) REVERT: B 181 ASP cc_start: 0.8610 (t0) cc_final: 0.8400 (t0) REVERT: B 202 ARG cc_start: 0.8897 (ttm110) cc_final: 0.8639 (ttm110) REVERT: A 137 GLN cc_start: 0.8885 (tp40) cc_final: 0.8340 (tt0) REVERT: A 138 LYS cc_start: 0.9201 (mttm) cc_final: 0.8951 (mmtp) REVERT: A 141 LEU cc_start: 0.8614 (mt) cc_final: 0.8404 (tp) REVERT: A 156 TYR cc_start: 0.8538 (m-10) cc_final: 0.7291 (m-10) REVERT: A 163 ASN cc_start: 0.9093 (t0) cc_final: 0.8615 (t0) REVERT: A 198 ASP cc_start: 0.8865 (t0) cc_final: 0.8650 (t0) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.1674 time to fit residues: 27.4033 Evaluate side-chains 97 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 44 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.096835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.068765 restraints weight = 12434.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.070521 restraints weight = 7042.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.071543 restraints weight = 4928.960| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4458 Z= 0.179 Angle : 0.583 7.030 6074 Z= 0.289 Chirality : 0.037 0.159 730 Planarity : 0.003 0.037 760 Dihedral : 4.016 13.797 606 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.22 % Allowed : 4.39 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.35), residues: 560 helix: 2.04 (0.25), residues: 386 sheet: 0.18 (0.66), residues: 50 loop : -2.67 (0.52), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 177 HIS 0.003 0.001 HIS A 73 PHE 0.010 0.001 PHE B 249 TYR 0.027 0.001 TYR A 175 ARG 0.013 0.001 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8309 (tm-30) REVERT: B 156 TYR cc_start: 0.8693 (m-10) cc_final: 0.8456 (m-10) REVERT: B 198 ASP cc_start: 0.8776 (t70) cc_final: 0.8570 (t0) REVERT: A 163 ASN cc_start: 0.9029 (t0) cc_final: 0.8535 (t0) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.1659 time to fit residues: 25.0474 Evaluate side-chains 97 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 0.0030 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.099424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.069301 restraints weight = 12419.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.071161 restraints weight = 7094.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.072273 restraints weight = 4996.847| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4458 Z= 0.154 Angle : 0.573 7.086 6074 Z= 0.280 Chirality : 0.036 0.169 730 Planarity : 0.003 0.031 760 Dihedral : 3.871 13.284 606 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: 1.64 (0.35), residues: 560 helix: 2.20 (0.25), residues: 388 sheet: 0.66 (0.68), residues: 50 loop : -2.58 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 178 HIS 0.002 0.001 HIS A 77 PHE 0.012 0.001 PHE B 101 TYR 0.013 0.001 TYR B 175 ARG 0.005 0.001 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 137 GLN cc_start: 0.8342 (tt0) cc_final: 0.7189 (tt0) REVERT: B 156 TYR cc_start: 0.8687 (m-10) cc_final: 0.7015 (m-10) REVERT: B 170 LEU cc_start: 0.9365 (tp) cc_final: 0.9050 (mt) REVERT: B 173 SER cc_start: 0.9033 (m) cc_final: 0.8822 (p) REVERT: A 93 MET cc_start: 0.8863 (mmm) cc_final: 0.8498 (mmm) REVERT: A 137 GLN cc_start: 0.8798 (tt0) cc_final: 0.8508 (tt0) REVERT: A 156 TYR cc_start: 0.8633 (m-10) cc_final: 0.7215 (m-10) REVERT: A 163 ASN cc_start: 0.8979 (t0) cc_final: 0.8696 (t0) REVERT: A 198 ASP cc_start: 0.8773 (t70) cc_final: 0.8453 (t0) REVERT: A 286 GLN cc_start: 0.6870 (tm-30) cc_final: 0.6381 (mp10) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1681 time to fit residues: 26.0470 Evaluate side-chains 106 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 1 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 50.0000 chunk 49 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.096514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.067413 restraints weight = 12243.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.069223 restraints weight = 7039.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.070379 restraints weight = 4980.142| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4458 Z= 0.191 Angle : 0.594 6.957 6074 Z= 0.295 Chirality : 0.038 0.171 730 Planarity : 0.004 0.036 760 Dihedral : 3.873 13.210 606 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.36), residues: 560 helix: 2.39 (0.25), residues: 390 sheet: 0.93 (0.67), residues: 50 loop : -2.72 (0.53), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 177 HIS 0.002 0.001 HIS A 73 PHE 0.011 0.001 PHE B 249 TYR 0.015 0.001 TYR B 175 ARG 0.007 0.001 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 173 SER cc_start: 0.9138 (m) cc_final: 0.8881 (p) REVERT: B 198 ASP cc_start: 0.8759 (t70) cc_final: 0.8520 (t0) REVERT: A 137 GLN cc_start: 0.8655 (tt0) cc_final: 0.7933 (tt0) REVERT: A 152 ASP cc_start: 0.7215 (t70) cc_final: 0.5970 (t70) REVERT: A 156 TYR cc_start: 0.8119 (m-10) cc_final: 0.7652 (m-10) REVERT: A 163 ASN cc_start: 0.9027 (t0) cc_final: 0.8701 (t0) REVERT: A 198 ASP cc_start: 0.8809 (t70) cc_final: 0.8361 (t0) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1710 time to fit residues: 25.6096 Evaluate side-chains 103 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 51 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.0970 chunk 22 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN A 71 HIS A 88 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.097920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.070026 restraints weight = 12748.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.071850 restraints weight = 7182.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.072991 restraints weight = 4991.577| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4458 Z= 0.167 Angle : 0.611 7.759 6074 Z= 0.296 Chirality : 0.037 0.170 730 Planarity : 0.003 0.032 760 Dihedral : 3.852 13.006 606 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.22 % Allowed : 2.19 % Favored : 97.59 % 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: 1.98 (0.36), residues: 560 helix: 2.46 (0.25), residues: 388 sheet: 1.10 (0.70), residues: 50 loop : -2.65 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 178 HIS 0.002 0.001 HIS A 77 PHE 0.009 0.001 PHE B 249 TYR 0.011 0.001 TYR A 102 ARG 0.006 0.000 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: B 102 TYR cc_start: 0.9384 (t80) cc_final: 0.9089 (t80) REVERT: B 156 TYR cc_start: 0.8115 (m-10) cc_final: 0.7769 (m-10) REVERT: B 173 SER cc_start: 0.9096 (m) cc_final: 0.8810 (p) REVERT: B 181 ASP cc_start: 0.8631 (t0) cc_final: 0.8311 (t0) REVERT: A 198 ASP cc_start: 0.8704 (t70) cc_final: 0.8351 (t0) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.1760 time to fit residues: 26.7448 Evaluate side-chains 105 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 HIS ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.099586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.070986 restraints weight = 12408.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.072848 restraints weight = 7075.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.074067 restraints weight = 4939.776| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.6436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4458 Z= 0.169 Angle : 0.616 7.070 6074 Z= 0.304 Chirality : 0.037 0.168 730 Planarity : 0.004 0.046 760 Dihedral : 3.834 14.984 606 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.22 % Allowed : 1.54 % Favored : 98.25 % 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: 1.91 (0.36), residues: 560 helix: 2.37 (0.25), residues: 390 sheet: 1.19 (0.70), residues: 50 loop : -2.66 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 177 HIS 0.001 0.000 HIS A 234 PHE 0.010 0.001 PHE A 101 TYR 0.014 0.001 TYR A 102 ARG 0.009 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.413 Fit side-chains REVERT: B 45 LEU cc_start: 0.9716 (tp) cc_final: 0.9501 (tt) REVERT: B 173 SER cc_start: 0.9028 (m) cc_final: 0.8730 (p) REVERT: B 181 ASP cc_start: 0.8590 (t0) cc_final: 0.8281 (t0) REVERT: B 198 ASP cc_start: 0.8661 (t70) cc_final: 0.8357 (t0) REVERT: A 93 MET cc_start: 0.8896 (mmm) cc_final: 0.8451 (mmm) REVERT: A 198 ASP cc_start: 0.8702 (t70) cc_final: 0.8362 (t0) outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 0.1638 time to fit residues: 24.6145 Evaluate side-chains 99 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN B 218 GLN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.096932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.069223 restraints weight = 12833.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.071120 restraints weight = 7018.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.072340 restraints weight = 4791.493| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.6505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4458 Z= 0.204 Angle : 0.650 6.817 6074 Z= 0.325 Chirality : 0.038 0.172 730 Planarity : 0.004 0.033 760 Dihedral : 3.867 14.408 606 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: 1.89 (0.36), residues: 560 helix: 2.36 (0.25), residues: 390 sheet: 1.07 (0.68), residues: 50 loop : -2.64 (0.53), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 177 HIS 0.002 0.001 HIS A 234 PHE 0.017 0.002 PHE A 101 TYR 0.014 0.001 TYR A 7 ARG 0.007 0.001 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.462 Fit side-chains REVERT: B 156 TYR cc_start: 0.8272 (m-10) cc_final: 0.7964 (m-10) REVERT: B 173 SER cc_start: 0.9185 (m) cc_final: 0.8858 (p) REVERT: B 181 ASP cc_start: 0.8752 (t0) cc_final: 0.8394 (t0) REVERT: B 198 ASP cc_start: 0.8836 (t70) cc_final: 0.8530 (t0) REVERT: A 93 MET cc_start: 0.8976 (mmm) cc_final: 0.8379 (mmm) REVERT: A 137 GLN cc_start: 0.8494 (tt0) cc_final: 0.8238 (tt0) REVERT: A 198 ASP cc_start: 0.8783 (t70) cc_final: 0.8404 (t0) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1504 time to fit residues: 21.9203 Evaluate side-chains 99 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 52 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 0.0470 chunk 27 optimal weight: 40.0000 chunk 28 optimal weight: 10.0000 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.096045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.067116 restraints weight = 12517.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.068935 restraints weight = 7161.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.070062 restraints weight = 5025.259| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4458 Z= 0.225 Angle : 0.672 7.291 6074 Z= 0.336 Chirality : 0.039 0.171 730 Planarity : 0.004 0.035 760 Dihedral : 3.939 14.696 606 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 1.82 (0.36), residues: 560 helix: 2.27 (0.25), residues: 392 sheet: 0.92 (0.66), residues: 50 loop : -2.53 (0.54), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 178 HIS 0.003 0.001 HIS A 234 PHE 0.018 0.002 PHE A 101 TYR 0.012 0.001 TYR A 102 ARG 0.006 0.001 ARG B 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.479 Fit side-chains REVERT: B 105 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8476 (tm-30) REVERT: B 156 TYR cc_start: 0.8251 (m-10) cc_final: 0.7959 (m-10) REVERT: B 173 SER cc_start: 0.9217 (m) cc_final: 0.8837 (p) REVERT: B 181 ASP cc_start: 0.8802 (t0) cc_final: 0.8417 (t0) REVERT: B 194 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8204 (tm-30) REVERT: B 195 GLN cc_start: 0.8843 (tt0) cc_final: 0.8464 (tt0) REVERT: B 198 ASP cc_start: 0.8831 (t70) cc_final: 0.8530 (t0) REVERT: A 105 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8438 (tm-30) REVERT: A 198 ASP cc_start: 0.8816 (t70) cc_final: 0.8320 (t0) REVERT: A 202 ARG cc_start: 0.8809 (ttm110) cc_final: 0.8601 (ttm110) REVERT: A 286 GLN cc_start: 0.6665 (tm-30) cc_final: 0.5870 (mp10) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1613 time to fit residues: 23.8124 Evaluate side-chains 103 residues out of total 456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 20.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.095316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.067666 restraints weight = 12681.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.069434 restraints weight = 7009.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.070452 restraints weight = 4839.803| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.6759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4458 Z= 0.219 Angle : 0.669 7.276 6074 Z= 0.331 Chirality : 0.038 0.165 730 Planarity : 0.003 0.033 760 Dihedral : 3.921 15.039 606 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 1.81 (0.36), residues: 560 helix: 2.28 (0.25), residues: 402 sheet: 0.81 (0.65), residues: 50 loop : -3.02 (0.54), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 10 HIS 0.003 0.001 HIS A 234 PHE 0.018 0.002 PHE A 101 TYR 0.025 0.002 TYR A 7 ARG 0.006 0.001 ARG B 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1608.05 seconds wall clock time: 29 minutes 27.45 seconds (1767.45 seconds total)