Starting phenix.real_space_refine on Thu Jul 2 10:39:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22ay_68141/07_2026/22ay_68141.cif Found real_map, /net/cci-nas-00/data/ceres_data/22ay_68141/07_2026/22ay_68141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/22ay_68141/07_2026/22ay_68141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22ay_68141/07_2026/22ay_68141.map" model { file = "/net/cci-nas-00/data/ceres_data/22ay_68141/07_2026/22ay_68141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22ay_68141/07_2026/22ay_68141.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.035 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 K 4 8.98 5 S 36 5.16 5 C 5416 2.51 5 N 1376 2.21 5 O 1324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8156 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2038 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 4, 'TRANS': 245} Chain breaks: 1 Chain: "B" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2038 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 4, 'TRANS': 245} Chain breaks: 1 Chain: "C" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2038 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 4, 'TRANS': 245} Chain breaks: 1 Chain: "D" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2038 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 4, 'TRANS': 245} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' K': 3} Chain breaks: 3 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Time building chain proxies: 1.41, per 1000 atoms: 0.17 Number of scatterers: 8156 At special positions: 0 Unit cell: (131.976, 131.976, 76.752, 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) K 4 19.00 S 36 16.00 O 1324 8.00 N 1376 7.00 C 5416 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: 0.56 Conformation dependent library (CDL) restraints added in 298.2 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1848 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 91.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.790A pdb=" N ARG A 75 " --> pdb=" O ASN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 92 through 114 removed outlier: 3.664A pdb=" N HIS A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 3.506A pdb=" N PHE A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 154 removed outlier: 5.216A pdb=" N CYS A 152 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG A 153 " --> pdb=" O CYS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.670A pdb=" N GLY A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 161 " --> pdb=" O TRP A 157 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 195 through 203 removed outlier: 3.587A pdb=" N SER A 199 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 211 removed outlier: 3.890A pdb=" N MET A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 255 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 329 removed outlier: 3.744A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'B' and resid 71 through 86 removed outlier: 3.790A pdb=" N ARG B 75 " --> pdb=" O ASN B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 92 through 114 removed outlier: 3.665A pdb=" N HIS B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 3.507A pdb=" N PHE B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 removed outlier: 5.217A pdb=" N CYS B 152 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG B 153 " --> pdb=" O CYS B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.670A pdb=" N GLY B 159 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 161 " --> pdb=" O TRP B 157 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 184 Processing helix chain 'B' and resid 195 through 203 removed outlier: 3.587A pdb=" N SER B 199 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 211 removed outlier: 3.891A pdb=" N MET B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 255 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 287 through 329 removed outlier: 3.744A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'C' and resid 71 through 86 removed outlier: 3.790A pdb=" N ARG C 75 " --> pdb=" O ASN C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 92 through 114 removed outlier: 3.664A pdb=" N HIS C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 removed outlier: 3.506A pdb=" N PHE C 142 " --> pdb=" O GLY C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 154 removed outlier: 5.216A pdb=" N CYS C 152 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG C 153 " --> pdb=" O CYS C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 165 removed outlier: 3.670A pdb=" N GLY C 159 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG C 160 " --> pdb=" O GLY C 156 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU C 161 " --> pdb=" O TRP C 157 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS C 162 " --> pdb=" O ARG C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 184 Processing helix chain 'C' and resid 195 through 203 removed outlier: 3.587A pdb=" N SER C 199 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 211 removed outlier: 3.891A pdb=" N MET C 208 " --> pdb=" O GLN C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 215 through 228 Processing helix chain 'C' and resid 228 through 255 Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 287 through 329 removed outlier: 3.743A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Proline residue: C 308 - end of helix Processing helix chain 'D' and resid 71 through 86 removed outlier: 3.791A pdb=" N ARG D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 92 through 114 removed outlier: 3.664A pdb=" N HIS D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 removed outlier: 3.506A pdb=" N PHE D 142 " --> pdb=" O GLY D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 154 removed outlier: 5.216A pdb=" N CYS D 152 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG D 153 " --> pdb=" O CYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 165 removed outlier: 3.670A pdb=" N GLY D 159 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU D 161 " --> pdb=" O TRP D 157 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 184 Processing helix chain 'D' and resid 195 through 203 removed outlier: 3.586A pdb=" N SER D 199 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 211 removed outlier: 3.891A pdb=" N MET D 208 " --> pdb=" O GLN D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 214 No H-bonds generated for 'chain 'D' and resid 212 through 214' Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 255 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 287 through 329 removed outlier: 3.744A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix 637 hydrogen bonds defined for protein. 1839 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: 1.01 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2464 1.34 - 1.46: 2273 1.46 - 1.58: 3591 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 8376 Sorted by residual: bond pdb=" CA ASP D 262 " pdb=" CB ASP D 262 " ideal model delta sigma weight residual 1.528 1.541 -0.012 1.56e-02 4.11e+03 6.23e-01 bond pdb=" CA ASP C 262 " pdb=" CB ASP C 262 " ideal model delta sigma weight residual 1.528 1.541 -0.012 1.56e-02 4.11e+03 6.09e-01 bond pdb=" CA ASP B 262 " pdb=" CB ASP B 262 " ideal model delta sigma weight residual 1.528 1.540 -0.012 1.56e-02 4.11e+03 5.51e-01 bond pdb=" CA ASP A 262 " pdb=" CB ASP A 262 " ideal model delta sigma weight residual 1.528 1.539 -0.011 1.56e-02 4.11e+03 4.89e-01 bond pdb=" CB ASP D 262 " pdb=" CG ASP D 262 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 4.16e-01 ... (remaining 8371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 11101 1.12 - 2.24: 183 2.24 - 3.36: 41 3.36 - 4.48: 7 4.48 - 5.60: 8 Bond angle restraints: 11340 Sorted by residual: angle pdb=" CA GLY D 156 " pdb=" C GLY D 156 " pdb=" O GLY D 156 " ideal model delta sigma weight residual 122.59 120.43 2.16 1.04e+00 9.25e-01 4.33e+00 angle pdb=" CA GLY B 156 " pdb=" C GLY B 156 " pdb=" O GLY B 156 " ideal model delta sigma weight residual 122.59 120.44 2.15 1.04e+00 9.25e-01 4.26e+00 angle pdb=" CA GLY C 156 " pdb=" C GLY C 156 " pdb=" O GLY C 156 " ideal model delta sigma weight residual 122.59 120.45 2.14 1.04e+00 9.25e-01 4.25e+00 angle pdb=" CA GLY A 156 " pdb=" C GLY A 156 " pdb=" O GLY A 156 " ideal model delta sigma weight residual 122.59 120.49 2.10 1.04e+00 9.25e-01 4.08e+00 angle pdb=" C GLU A 86 " pdb=" N ARG A 87 " pdb=" CA ARG A 87 " ideal model delta sigma weight residual 123.15 120.83 2.32 1.21e+00 6.83e-01 3.68e+00 ... (remaining 11335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4312 17.90 - 35.80: 368 35.80 - 53.69: 68 53.69 - 71.59: 12 71.59 - 89.49: 8 Dihedral angle restraints: 4768 sinusoidal: 1872 harmonic: 2896 Sorted by residual: dihedral pdb=" CB GLU A 86 " pdb=" CG GLU A 86 " pdb=" CD GLU A 86 " pdb=" OE1 GLU A 86 " ideal model delta sinusoidal sigma weight residual 0.00 89.49 -89.49 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU D 86 " pdb=" CG GLU D 86 " pdb=" CD GLU D 86 " pdb=" OE1 GLU D 86 " ideal model delta sinusoidal sigma weight residual 0.00 89.48 -89.48 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 86 " pdb=" CG GLU B 86 " pdb=" CD GLU B 86 " pdb=" OE1 GLU B 86 " ideal model delta sinusoidal sigma weight residual 0.00 89.47 -89.47 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 4765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 719 0.024 - 0.047: 321 0.047 - 0.071: 173 0.071 - 0.095: 19 0.095 - 0.119: 16 Chirality restraints: 1248 Sorted by residual: chirality pdb=" CA ILE B 115 " pdb=" N ILE B 115 " pdb=" C ILE B 115 " pdb=" CB ILE B 115 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA ILE C 115 " pdb=" N ILE C 115 " pdb=" C ILE C 115 " pdb=" CB ILE C 115 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA ILE D 115 " pdb=" N ILE D 115 " pdb=" C ILE D 115 " pdb=" CB ILE D 115 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 1245 not shown) Planarity restraints: 1372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 329 " -0.010 2.00e-02 2.50e+03 1.21e-02 2.55e+00 pdb=" CG PHE D 329 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE D 329 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE D 329 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE D 329 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 329 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 329 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 329 " 0.010 2.00e-02 2.50e+03 1.20e-02 2.50e+00 pdb=" CG PHE B 329 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE B 329 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 329 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 329 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 329 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 329 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 329 " 0.010 2.00e-02 2.50e+03 1.19e-02 2.48e+00 pdb=" CG PHE C 329 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE C 329 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 329 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 329 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 329 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 329 " 0.001 2.00e-02 2.50e+03 ... (remaining 1369 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.90: 3133 2.90 - 3.46: 9522 3.46 - 4.02: 15160 4.02 - 4.58: 22583 4.58 - 5.14: 29414 Nonbonded interactions: 79812 Sorted by model distance: nonbonded pdb=" OH TYR C 95 " pdb=" OE1 GLU C 140 " model vdw 2.346 3.040 nonbonded pdb=" OH TYR B 95 " pdb=" OE1 GLU B 140 " model vdw 2.346 3.040 nonbonded pdb=" OH TYR A 95 " pdb=" OE1 GLU A 140 " model vdw 2.346 3.040 nonbonded pdb=" OH TYR D 95 " pdb=" OE1 GLU D 140 " model vdw 2.347 3.040 nonbonded pdb=" OE1 GLN A 204 " pdb=" NH1 ARG A 207 " model vdw 2.377 3.120 ... (remaining 79807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 70 through 329) selection = chain 'B' selection = (chain 'C' and resid 70 through 329) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.010 Set scattering table: 0.010 Process input model: 6.770 Find NCS groups from input model: 0.110 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:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 : 0.002 0.017 8376 Z= 0.085 Angle : 0.407 5.598 11340 Z= 0.238 Chirality : 0.033 0.119 1248 Planarity : 0.003 0.027 1372 Dihedral : 14.344 89.488 2920 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 0.00 % Allowed : 13.88 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 984 helix: 0.46 (0.16), residues: 808 sheet: None (None), residues: 0 loop : 1.32 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 165 TYR 0.009 0.001 TYR D 280 PHE 0.028 0.001 PHE D 329 TRP 0.013 0.001 TRP C 270 HIS 0.002 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.09 ( 8376) covalent geometry : angle 0.40737 / 0.24 (11340) hydrogen bonds : bond 0.21777 / 14.01 ( 637) hydrogen bonds : angle 6.63625 / 4.89 ( 1839) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.298 Fit side-chains REVERT: A 89 ARG cc_start: 0.7006 (mtm-85) cc_final: 0.6476 (ttp-110) REVERT: A 262 ASP cc_start: 0.8317 (t0) cc_final: 0.8054 (t70) REVERT: B 89 ARG cc_start: 0.7017 (mtm-85) cc_final: 0.6482 (ttp-110) REVERT: B 262 ASP cc_start: 0.8316 (t0) cc_final: 0.8057 (t70) REVERT: C 89 ARG cc_start: 0.7019 (mtm-85) cc_final: 0.6488 (ttp-110) REVERT: C 262 ASP cc_start: 0.8313 (t0) cc_final: 0.8055 (t70) REVERT: D 89 ARG cc_start: 0.7013 (mtm-85) cc_final: 0.6479 (ttp-110) REVERT: D 262 ASP cc_start: 0.8315 (t0) cc_final: 0.8055 (t70) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.5472 time to fit residues: 64.3314 Evaluate side-chains 97 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.0030 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.192385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122943 restraints weight = 7826.654| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.89 r_work: 0.3289 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 8376 Z= 0.118 Angle : 0.442 4.916 11340 Z= 0.252 Chirality : 0.037 0.134 1248 Planarity : 0.003 0.023 1372 Dihedral : 3.701 11.929 1120 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.36 % Allowed : 12.08 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.25), residues: 984 helix: 1.45 (0.17), residues: 812 sheet: None (None), residues: 0 loop : 1.21 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 165 TYR 0.010 0.001 TYR D 74 PHE 0.009 0.001 PHE A 316 TRP 0.013 0.001 TRP A 270 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 ( 8376) covalent geometry : angle 0.44216 / 0.25 (11340) hydrogen bonds : bond 0.04661 / 2.98 ( 637) hydrogen bonds : angle 4.23736 / 3.12 ( 1839) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.289 Fit side-chains REVERT: A 89 ARG cc_start: 0.6937 (mtm-85) cc_final: 0.6104 (ttp-110) REVERT: A 262 ASP cc_start: 0.8143 (t0) cc_final: 0.7818 (t70) REVERT: B 89 ARG cc_start: 0.6929 (mtm-85) cc_final: 0.6109 (ttp-110) REVERT: B 262 ASP cc_start: 0.8122 (t0) cc_final: 0.7794 (t70) REVERT: C 89 ARG cc_start: 0.6943 (mtm-85) cc_final: 0.6100 (ttp-110) REVERT: C 262 ASP cc_start: 0.8133 (t0) cc_final: 0.7805 (t70) REVERT: D 89 ARG cc_start: 0.6929 (mtm-85) cc_final: 0.6094 (ttp-110) REVERT: D 262 ASP cc_start: 0.8134 (t0) cc_final: 0.7807 (t70) outliers start: 3 outliers final: 3 residues processed: 117 average time/residue: 0.4626 time to fit residues: 57.5820 Evaluate side-chains 108 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain D residue 319 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 GLN B 326 GLN C 326 GLN D 326 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.186779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115280 restraints weight = 7603.540| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.87 r_work: 0.3200 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8376 Z= 0.201 Angle : 0.511 4.894 11340 Z= 0.288 Chirality : 0.041 0.143 1248 Planarity : 0.004 0.032 1372 Dihedral : 3.995 16.360 1120 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.39 % Allowed : 12.56 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.26), residues: 984 helix: 1.34 (0.18), residues: 812 sheet: None (None), residues: 0 loop : 1.12 (0.50), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 165 TYR 0.011 0.001 TYR D 74 PHE 0.012 0.002 PHE C 316 TRP 0.014 0.001 TRP A 270 HIS 0.004 0.002 HIS C 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 ( 8376) covalent geometry : angle 0.51131 / 0.29 (11340) hydrogen bonds : bond 0.04970 / 3.17 ( 637) hydrogen bonds : angle 4.38549 / 3.23 ( 1839) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.289 Fit side-chains REVERT: A 89 ARG cc_start: 0.6961 (mtm-85) cc_final: 0.6156 (ttp-110) REVERT: A 162 LYS cc_start: 0.7058 (ttmt) cc_final: 0.6760 (tttp) REVERT: B 89 ARG cc_start: 0.6967 (mtm-85) cc_final: 0.6161 (ttp-110) REVERT: B 162 LYS cc_start: 0.7062 (ttmt) cc_final: 0.6761 (tttp) REVERT: C 89 ARG cc_start: 0.6962 (mtm-85) cc_final: 0.6150 (ttp-110) REVERT: C 162 LYS cc_start: 0.7083 (ttmt) cc_final: 0.6782 (tttp) REVERT: D 89 ARG cc_start: 0.6957 (mtm-85) cc_final: 0.6152 (ttp-110) REVERT: D 162 LYS cc_start: 0.7080 (ttmt) cc_final: 0.6780 (tttp) outliers start: 20 outliers final: 12 residues processed: 126 average time/residue: 0.5303 time to fit residues: 70.0868 Evaluate side-chains 118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 319 LYS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain C residue 319 LYS Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 319 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 52 optimal weight: 0.0570 chunk 38 optimal weight: 5.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.189715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119385 restraints weight = 7846.026| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.90 r_work: 0.3249 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8376 Z= 0.129 Angle : 0.445 4.832 11340 Z= 0.249 Chirality : 0.037 0.126 1248 Planarity : 0.003 0.035 1372 Dihedral : 3.768 13.709 1120 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 2.27 % Allowed : 14.95 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.26), residues: 984 helix: 1.88 (0.18), residues: 776 sheet: None (None), residues: 0 loop : 2.47 (0.50), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 165 TYR 0.010 0.001 TYR A 280 PHE 0.008 0.001 PHE C 137 TRP 0.012 0.001 TRP D 270 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 8376) covalent geometry : angle 0.44480 / 0.25 (11340) hydrogen bonds : bond 0.04228 / 2.69 ( 637) hydrogen bonds : angle 4.10727 / 3.03 ( 1839) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.199 Fit side-chains REVERT: A 89 ARG cc_start: 0.7014 (mtm-85) cc_final: 0.6192 (ttp-110) REVERT: A 121 SER cc_start: 0.7148 (OUTLIER) cc_final: 0.6899 (p) REVERT: A 162 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6769 (tttp) REVERT: B 89 ARG cc_start: 0.7027 (mtm-85) cc_final: 0.6197 (ttp-110) REVERT: B 121 SER cc_start: 0.7158 (OUTLIER) cc_final: 0.6913 (p) REVERT: B 162 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6758 (tttp) REVERT: C 89 ARG cc_start: 0.7016 (mtm-85) cc_final: 0.6193 (ttp-110) REVERT: C 121 SER cc_start: 0.7155 (OUTLIER) cc_final: 0.6908 (p) REVERT: C 162 LYS cc_start: 0.7010 (ttmt) cc_final: 0.6708 (tttp) REVERT: D 89 ARG cc_start: 0.7017 (mtm-85) cc_final: 0.6189 (ttp-110) REVERT: D 121 SER cc_start: 0.7150 (OUTLIER) cc_final: 0.6902 (p) REVERT: D 162 LYS cc_start: 0.7045 (ttmt) cc_final: 0.6751 (tttp) outliers start: 19 outliers final: 4 residues processed: 128 average time/residue: 0.4706 time to fit residues: 63.7264 Evaluate side-chains 118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 260 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.188614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118141 restraints weight = 7734.869| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.90 r_work: 0.3237 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8376 Z= 0.143 Angle : 0.462 4.856 11340 Z= 0.259 Chirality : 0.038 0.145 1248 Planarity : 0.003 0.036 1372 Dihedral : 3.801 14.296 1120 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.03 % Allowed : 15.19 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.26), residues: 984 helix: 1.55 (0.18), residues: 816 sheet: None (None), residues: 0 loop : 1.24 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 165 TYR 0.010 0.001 TYR D 74 PHE 0.009 0.001 PHE D 137 TRP 0.012 0.001 TRP C 270 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 8376) covalent geometry : angle 0.46166 / 0.26 (11340) hydrogen bonds : bond 0.04310 / 2.75 ( 637) hydrogen bonds : angle 4.12784 / 3.05 ( 1839) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.263 Fit side-chains REVERT: A 89 ARG cc_start: 0.7034 (mtm-85) cc_final: 0.6168 (ttp-110) REVERT: A 121 SER cc_start: 0.7162 (OUTLIER) cc_final: 0.6919 (p) REVERT: A 162 LYS cc_start: 0.7061 (ttmt) cc_final: 0.6776 (tttp) REVERT: B 89 ARG cc_start: 0.7041 (mtm-85) cc_final: 0.6173 (ttp-110) REVERT: B 121 SER cc_start: 0.7167 (OUTLIER) cc_final: 0.6927 (p) REVERT: B 162 LYS cc_start: 0.7063 (ttmt) cc_final: 0.6777 (tttp) REVERT: C 89 ARG cc_start: 0.7020 (mtm-85) cc_final: 0.6183 (ttp-110) REVERT: C 121 SER cc_start: 0.7172 (OUTLIER) cc_final: 0.6930 (p) REVERT: C 162 LYS cc_start: 0.7030 (ttmt) cc_final: 0.6730 (tttp) REVERT: D 89 ARG cc_start: 0.7038 (mtm-85) cc_final: 0.6201 (ttp-110) REVERT: D 121 SER cc_start: 0.7159 (OUTLIER) cc_final: 0.6918 (p) REVERT: D 162 LYS cc_start: 0.7059 (ttmt) cc_final: 0.6764 (tttp) outliers start: 17 outliers final: 8 residues processed: 117 average time/residue: 0.4980 time to fit residues: 61.5579 Evaluate side-chains 112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 47 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.189402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.119581 restraints weight = 7704.547| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.89 r_work: 0.3253 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8376 Z= 0.128 Angle : 0.438 4.843 11340 Z= 0.249 Chirality : 0.037 0.126 1248 Planarity : 0.003 0.037 1372 Dihedral : 3.737 13.890 1120 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.75 % Allowed : 13.28 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.27), residues: 984 helix: 1.97 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 2.58 (0.52), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 165 TYR 0.010 0.001 TYR A 74 PHE 0.008 0.001 PHE D 137 TRP 0.011 0.001 TRP A 270 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 8376) covalent geometry : angle 0.43760 / 0.25 (11340) hydrogen bonds : bond 0.04121 / 2.62 ( 637) hydrogen bonds : angle 4.03705 / 2.98 ( 1839) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.245 Fit side-chains REVERT: A 89 ARG cc_start: 0.7036 (mtm-85) cc_final: 0.6160 (ttp-110) REVERT: A 121 SER cc_start: 0.7147 (OUTLIER) cc_final: 0.6937 (p) REVERT: A 162 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6800 (tttp) REVERT: A 208 MET cc_start: 0.7218 (mtp) cc_final: 0.7016 (mtp) REVERT: B 89 ARG cc_start: 0.7039 (mtm-85) cc_final: 0.6161 (ttp-110) REVERT: B 121 SER cc_start: 0.7147 (OUTLIER) cc_final: 0.6947 (p) REVERT: B 162 LYS cc_start: 0.7074 (ttmt) cc_final: 0.6794 (tttp) REVERT: B 208 MET cc_start: 0.7220 (mtp) cc_final: 0.7017 (mtp) REVERT: C 89 ARG cc_start: 0.7042 (mtm-85) cc_final: 0.6165 (ttp-110) REVERT: C 121 SER cc_start: 0.7155 (OUTLIER) cc_final: 0.6946 (p) REVERT: C 162 LYS cc_start: 0.7002 (ttmt) cc_final: 0.6718 (tttp) REVERT: D 89 ARG cc_start: 0.7032 (mtm-85) cc_final: 0.6156 (ttp-110) REVERT: D 121 SER cc_start: 0.7148 (OUTLIER) cc_final: 0.6940 (p) REVERT: D 162 LYS cc_start: 0.7019 (ttmt) cc_final: 0.6737 (tttp) REVERT: D 208 MET cc_start: 0.7217 (mtp) cc_final: 0.7016 (mtp) outliers start: 23 outliers final: 8 residues processed: 119 average time/residue: 0.4809 time to fit residues: 60.6377 Evaluate side-chains 109 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 9 optimal weight: 0.0170 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.190179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120680 restraints weight = 7831.064| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.90 r_work: 0.3269 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8376 Z= 0.119 Angle : 0.426 4.835 11340 Z= 0.242 Chirality : 0.036 0.123 1248 Planarity : 0.003 0.038 1372 Dihedral : 3.693 13.458 1120 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.15 % Allowed : 14.00 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.27), residues: 984 helix: 2.06 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 2.53 (0.52), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 165 TYR 0.009 0.001 TYR A 74 PHE 0.008 0.001 PHE D 137 TRP 0.011 0.001 TRP A 270 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 8376) covalent geometry : angle 0.42611 / 0.24 (11340) hydrogen bonds : bond 0.03994 / 2.54 ( 637) hydrogen bonds : angle 3.96695 / 2.93 ( 1839) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.303 Fit side-chains REVERT: A 89 ARG cc_start: 0.7014 (mtm-85) cc_final: 0.6146 (ttp-110) REVERT: A 153 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6674 (mtm110) REVERT: A 162 LYS cc_start: 0.7084 (ttmt) cc_final: 0.6816 (tttp) REVERT: A 208 MET cc_start: 0.7239 (mtp) cc_final: 0.7026 (mtp) REVERT: B 89 ARG cc_start: 0.7010 (mtm-85) cc_final: 0.6188 (ttp-110) REVERT: B 153 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6670 (mtm110) REVERT: B 162 LYS cc_start: 0.7075 (ttmt) cc_final: 0.6809 (tttp) REVERT: B 208 MET cc_start: 0.7239 (mtp) cc_final: 0.7027 (mtp) REVERT: C 89 ARG cc_start: 0.7034 (mtm-85) cc_final: 0.6158 (ttp-110) REVERT: C 162 LYS cc_start: 0.7024 (ttmt) cc_final: 0.6750 (tttp) REVERT: D 89 ARG cc_start: 0.7004 (mtm-85) cc_final: 0.6183 (ttp-110) REVERT: D 162 LYS cc_start: 0.7024 (ttmt) cc_final: 0.6749 (tttp) REVERT: D 208 MET cc_start: 0.7245 (mtp) cc_final: 0.7034 (mtp) outliers start: 18 outliers final: 11 residues processed: 129 average time/residue: 0.4732 time to fit residues: 64.6785 Evaluate side-chains 110 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.188397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118454 restraints weight = 7704.286| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.89 r_work: 0.3239 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8376 Z= 0.140 Angle : 0.452 4.849 11340 Z= 0.257 Chirality : 0.037 0.124 1248 Planarity : 0.003 0.039 1372 Dihedral : 3.761 14.218 1120 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.67 % Allowed : 15.19 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.27), residues: 984 helix: 1.97 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 2.57 (0.52), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 165 TYR 0.010 0.001 TYR A 74 PHE 0.009 0.001 PHE A 137 TRP 0.011 0.001 TRP C 270 HIS 0.004 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 8376) covalent geometry : angle 0.45242 / 0.26 (11340) hydrogen bonds : bond 0.04193 / 2.67 ( 637) hydrogen bonds : angle 4.07260 / 3.00 ( 1839) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.239 Fit side-chains REVERT: A 89 ARG cc_start: 0.7026 (mtm-85) cc_final: 0.6243 (ttp-110) REVERT: A 153 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6632 (mtm110) REVERT: A 162 LYS cc_start: 0.7095 (ttmt) cc_final: 0.6827 (tttp) REVERT: A 208 MET cc_start: 0.7259 (mtp) cc_final: 0.7056 (mtp) REVERT: B 89 ARG cc_start: 0.6980 (mtm-85) cc_final: 0.6225 (ttp-110) REVERT: B 153 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6647 (mtm110) REVERT: B 162 LYS cc_start: 0.7085 (ttmt) cc_final: 0.6822 (tttp) REVERT: B 208 MET cc_start: 0.7258 (mtp) cc_final: 0.7056 (mtp) REVERT: C 89 ARG cc_start: 0.7049 (mtm-85) cc_final: 0.6248 (ttp-110) REVERT: C 162 LYS cc_start: 0.7020 (ttmt) cc_final: 0.6750 (tttp) REVERT: D 89 ARG cc_start: 0.7057 (mtm-85) cc_final: 0.6249 (ttp-110) REVERT: D 162 LYS cc_start: 0.7015 (ttmt) cc_final: 0.6746 (tttp) REVERT: D 208 MET cc_start: 0.7261 (mtp) cc_final: 0.7059 (mtp) outliers start: 14 outliers final: 8 residues processed: 114 average time/residue: 0.5321 time to fit residues: 63.9786 Evaluate side-chains 114 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 96 optimal weight: 0.0870 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.190461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121211 restraints weight = 7769.428| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.91 r_work: 0.3272 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8376 Z= 0.114 Angle : 0.422 4.807 11340 Z= 0.240 Chirality : 0.036 0.119 1248 Planarity : 0.003 0.038 1372 Dihedral : 3.662 12.959 1120 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 1.67 % Allowed : 15.19 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.25 (0.27), residues: 984 helix: 2.13 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 2.60 (0.52), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 165 TYR 0.009 0.001 TYR C 237 PHE 0.008 0.001 PHE C 137 TRP 0.010 0.001 TRP B 270 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 8376) covalent geometry : angle 0.42250 / 0.24 (11340) hydrogen bonds : bond 0.03889 / 2.48 ( 637) hydrogen bonds : angle 3.95216 / 2.92 ( 1839) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.208 Fit side-chains REVERT: A 89 ARG cc_start: 0.6932 (mtm-85) cc_final: 0.6139 (ttp-110) REVERT: A 153 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6623 (mtm110) REVERT: A 162 LYS cc_start: 0.7052 (ttmt) cc_final: 0.6767 (tttp) REVERT: B 89 ARG cc_start: 0.6942 (mtm-85) cc_final: 0.6147 (ttp-110) REVERT: B 153 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6586 (mtm110) REVERT: B 162 LYS cc_start: 0.7042 (ttmt) cc_final: 0.6761 (tttp) REVERT: C 89 ARG cc_start: 0.6941 (mtm-85) cc_final: 0.6150 (ttp-110) REVERT: C 162 LYS cc_start: 0.7041 (ttmt) cc_final: 0.6747 (tttp) REVERT: D 89 ARG cc_start: 0.6942 (mtm-85) cc_final: 0.6149 (ttp-110) REVERT: D 162 LYS cc_start: 0.7042 (ttmt) cc_final: 0.6743 (tttp) outliers start: 14 outliers final: 12 residues processed: 113 average time/residue: 0.4925 time to fit residues: 58.8488 Evaluate side-chains 117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 38 optimal weight: 0.0470 chunk 61 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.189250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119657 restraints weight = 7744.825| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.90 r_work: 0.3258 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8376 Z= 0.128 Angle : 0.441 4.831 11340 Z= 0.250 Chirality : 0.037 0.161 1248 Planarity : 0.003 0.038 1372 Dihedral : 3.714 13.745 1120 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.67 % Allowed : 16.51 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.27), residues: 984 helix: 2.02 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 2.65 (0.53), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 165 TYR 0.009 0.001 TYR D 74 PHE 0.009 0.001 PHE D 137 TRP 0.011 0.001 TRP C 270 HIS 0.004 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 8376) covalent geometry : angle 0.44093 / 0.25 (11340) hydrogen bonds : bond 0.04049 / 2.58 ( 637) hydrogen bonds : angle 4.02430 / 2.97 ( 1839) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.192 Fit side-chains REVERT: A 89 ARG cc_start: 0.6953 (mtm-85) cc_final: 0.6144 (ttp-110) REVERT: A 153 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6587 (mtm180) REVERT: A 162 LYS cc_start: 0.7105 (ttmt) cc_final: 0.6855 (tttp) REVERT: B 89 ARG cc_start: 0.6955 (mtm-85) cc_final: 0.6181 (ttp-110) REVERT: B 153 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6578 (mtm180) REVERT: B 162 LYS cc_start: 0.7084 (ttmt) cc_final: 0.6837 (tttp) REVERT: C 89 ARG cc_start: 0.6964 (mtm-85) cc_final: 0.6189 (ttp-110) REVERT: C 162 LYS cc_start: 0.7087 (ttmt) cc_final: 0.6842 (tttp) REVERT: D 89 ARG cc_start: 0.6962 (mtm-85) cc_final: 0.6185 (ttp-110) REVERT: D 162 LYS cc_start: 0.7082 (ttmt) cc_final: 0.6839 (tttp) outliers start: 14 outliers final: 7 residues processed: 114 average time/residue: 0.5002 time to fit residues: 60.4374 Evaluate side-chains 117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain D residue 260 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 0.0070 chunk 89 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.190450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121346 restraints weight = 7800.874| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.92 r_work: 0.3281 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8376 Z= 0.114 Angle : 0.428 4.817 11340 Z= 0.243 Chirality : 0.036 0.156 1248 Planarity : 0.003 0.038 1372 Dihedral : 3.660 12.956 1120 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 1.08 % Allowed : 17.11 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.24 (0.27), residues: 984 helix: 2.11 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 2.64 (0.53), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 165 TYR 0.009 0.001 TYR C 74 PHE 0.008 0.001 PHE A 137 TRP 0.010 0.001 TRP A 270 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 8376) covalent geometry : angle 0.42819 / 0.24 (11340) hydrogen bonds : bond 0.03889 / 2.47 ( 637) hydrogen bonds : angle 3.95335 / 2.92 ( 1839) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3885.46 seconds wall clock time: 66 minutes 28.60 seconds (3988.60 seconds total)