Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:32:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vrf_8728/11_2022/5vrf_8728.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vrf_8728/11_2022/5vrf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vrf_8728/11_2022/5vrf_8728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vrf_8728/11_2022/5vrf_8728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vrf_8728/11_2022/5vrf_8728.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vrf_8728/11_2022/5vrf_8728.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/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: 2.97, per 1000 atoms: 0.68 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 - 3.50 Amino acid : False - 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: 2.22 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.15 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: 1.17 Time building geometry restraints manager: 2.41 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: 99.05 - 106.28: 105 106.28 - 113.52: 2525 113.52 - 120.75: 2093 120.75 - 127.98: 1309 127.98 - 135.22: 42 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 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 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. 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: 0.120 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: 0.000 Extract box with map and model: 0.900 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 17.770 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2397 time to fit residues: 48.6601 Evaluate side-chains 84 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.477 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5983 ------------------------------------------------------------------------------- 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: 3.9990 chunk 42 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 205 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 4458 Z= 0.287 Angle : 0.650 7.276 6074 Z= 0.343 Chirality : 0.038 0.174 730 Planarity : 0.005 0.047 760 Dihedral : 4.664 15.286 606 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 0.00 % 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: -0.81 (0.32), residues: 560 helix: 0.38 (0.24), residues: 392 sheet: -0.97 (0.61), residues: 50 loop : -3.32 (0.46), residues: 118 *********************** 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 134 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1868 time to fit residues: 30.3721 Evaluate side-chains 91 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 50 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 195 GLN A 71 HIS ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 4458 Z= 0.282 Angle : 0.632 7.455 6074 Z= 0.324 Chirality : 0.038 0.163 730 Planarity : 0.004 0.044 760 Dihedral : 4.322 13.711 606 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.00 % 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: 0.64 (0.35), residues: 560 helix: 1.58 (0.25), residues: 388 sheet: -0.72 (0.60), residues: 50 loop : -2.95 (0.50), residues: 122 *********************** 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 111 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1606 time to fit residues: 22.4923 Evaluate side-chains 88 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.527 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 4458 Z= 0.269 Angle : 0.617 7.216 6074 Z= 0.312 Chirality : 0.037 0.161 730 Planarity : 0.004 0.042 760 Dihedral : 4.263 13.839 606 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 0.00 % 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: 1.06 (0.35), residues: 560 helix: 1.89 (0.26), residues: 390 sheet: -0.23 (0.65), residues: 50 loop : -3.03 (0.49), residues: 120 *********************** 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 105 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1678 time to fit residues: 22.0808 Evaluate side-chains 83 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.516 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 48 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN B 163 ASN B 195 GLN ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 4458 Z= 0.173 Angle : 0.582 6.935 6074 Z= 0.290 Chirality : 0.037 0.170 730 Planarity : 0.003 0.035 760 Dihedral : 3.985 13.409 606 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 0.22 % 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: 1.61 (0.35), residues: 560 helix: 2.27 (0.25), residues: 388 sheet: 0.27 (0.68), residues: 50 loop : -2.78 (0.51), residues: 122 *********************** 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 114 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.1540 time to fit residues: 22.0965 Evaluate side-chains 94 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.530 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN B 163 ASN B 195 GLN A 137 GLN A 163 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.6117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 4458 Z= 0.186 Angle : 0.589 6.960 6074 Z= 0.296 Chirality : 0.037 0.162 730 Planarity : 0.003 0.036 760 Dihedral : 3.959 13.474 606 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 0.22 % 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: 1.70 (0.36), residues: 560 helix: 2.34 (0.26), residues: 386 sheet: 0.44 (0.68), residues: 50 loop : -2.71 (0.48), residues: 124 *********************** 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 112 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1515 time to fit residues: 21.2198 Evaluate side-chains 91 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.497 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN B 163 ASN B 195 GLN ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN A 163 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.6304 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= 0.168 Angle : 0.599 7.719 6074 Z= 0.291 Chirality : 0.037 0.159 730 Planarity : 0.003 0.034 760 Dihedral : 3.926 13.363 606 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.36), residues: 560 helix: 2.39 (0.25), residues: 386 sheet: 0.60 (0.68), residues: 50 loop : -2.68 (0.49), residues: 124 *********************** 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 115 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.1586 time to fit residues: 22.7811 Evaluate side-chains 98 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.520 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 0.0770 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- 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 137 GLN B 163 ASN B 195 GLN ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN A 286 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.6499 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= 0.182 Angle : 0.616 6.886 6074 Z= 0.302 Chirality : 0.036 0.173 730 Planarity : 0.004 0.048 760 Dihedral : 3.870 13.427 606 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 0.22 % 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: 1.87 (0.36), residues: 560 helix: 2.45 (0.26), residues: 392 sheet: 0.69 (0.67), residues: 50 loop : -2.98 (0.48), residues: 118 *********************** 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 116 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.1648 time to fit residues: 24.2849 Evaluate side-chains 95 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.491 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.1980 chunk 47 optimal weight: 4.9990 chunk 50 optimal weight: 40.0000 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN B 163 ASN A 71 HIS ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.6641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 4458 Z= 0.171 Angle : 0.617 7.731 6074 Z= 0.300 Chirality : 0.036 0.168 730 Planarity : 0.004 0.050 760 Dihedral : 3.821 12.955 606 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 0.00 % 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: 2.01 (0.36), residues: 560 helix: 2.55 (0.26), residues: 388 sheet: 0.71 (0.66), residues: 50 loop : -2.72 (0.50), residues: 122 *********************** 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 116 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1539 time to fit residues: 22.5369 Evaluate side-chains 94 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.526 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 0.0670 chunk 47 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7924 ------------------------------------------------------------------------------- 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 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.6750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4458 Z= 0.182 Angle : 0.653 8.132 6074 Z= 0.312 Chirality : 0.037 0.184 730 Planarity : 0.004 0.044 760 Dihedral : 3.808 13.144 606 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 0.00 % 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: 2.12 (0.36), residues: 560 helix: 2.66 (0.25), residues: 388 sheet: 0.65 (0.67), residues: 50 loop : -2.72 (0.50), residues: 122 ********************** 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 115 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1651 time to fit residues: 23.7782 Evaluate side-chains 95 residues out of total 456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 40.0000 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.098819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.069406 restraints weight = 12131.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.071252 restraints weight = 7047.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.072383 restraints weight = 4993.523| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.6871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4458 Z= 0.179 Angle : 0.652 7.730 6074 Z= 0.316 Chirality : 0.037 0.163 730 Planarity : 0.004 0.046 760 Dihedral : 3.785 13.287 606 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 0.00 % 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: 2.10 (0.36), residues: 560 helix: 2.60 (0.25), residues: 388 sheet: 0.67 (0.66), residues: 50 loop : -2.56 (0.51), residues: 122 =============================================================================== Job complete usr+sys time: 1118.35 seconds wall clock time: 20 minutes 59.14 seconds (1259.14 seconds total)