Starting phenix.real_space_refine on Wed Aug 5 03:20:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22ay_68141/08_2026/22ay_68141.cif Found real_map, /net/cci-nas-00/data/ceres_data/22ay_68141/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/22ay_68141/08_2026/22ay_68141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22ay_68141/08_2026/22ay_68141.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22ay_68141/08_2026/22ay_68141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22ay_68141/08_2026/22ay_68141.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.90, per 1000 atoms: 0.23 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: 0.60 Conformation dependent library (CDL) restraints added in 428.5 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: 0.20 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: 1.34 Time building geometry restraints manager: 0.86 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: 1.780 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 8.410 Find NCS groups from input model: 0.170 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.110 ------------------------------------------------------------------------------- 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 : 0.308 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: 0.7368 time to fit residues: 86.5514 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 : 0.287 ------------------------------------------------------------------------------- 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: 0.8980 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.192157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.121093 restraints weight = 7658.288| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.86 r_work: 0.3266 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1419 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= 0.117 Angle : 0.430 5.011 11340 Z= 0.246 Chirality : 0.037 0.127 1248 Planarity : 0.003 0.023 1372 Dihedral : 3.671 11.934 1120 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.48 % Allowed : 11.96 % 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: 2.03 (0.25), residues: 984 helix: 1.45 (0.17), residues: 812 sheet: None (None), residues: 0 loop : 1.27 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 165 TYR 0.009 0.001 TYR A 74 PHE 0.010 0.001 PHE A 316 TRP 0.013 0.001 TRP C 270 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.12 ( 8376) covalent geometry : angle 0.43047 / 0.25 (11340) hydrogen bonds : bond 0.04727 / 3.02 ( 637) hydrogen bonds : angle 4.21729 / 3.11 ( 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 121 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.311 Fit side-chains REVERT: A 89 ARG cc_start: 0.6918 (mtm-85) cc_final: 0.6088 (ttp-110) REVERT: A 262 ASP cc_start: 0.8108 (t0) cc_final: 0.7771 (t70) REVERT: B 89 ARG cc_start: 0.6904 (mtm-85) cc_final: 0.6088 (ttp-110) REVERT: B 262 ASP cc_start: 0.8096 (t0) cc_final: 0.7762 (t70) REVERT: C 89 ARG cc_start: 0.6917 (mtm-85) cc_final: 0.6080 (ttp-110) REVERT: C 262 ASP cc_start: 0.8103 (t0) cc_final: 0.7770 (t70) REVERT: D 89 ARG cc_start: 0.6911 (mtm-85) cc_final: 0.6080 (ttp-110) REVERT: D 262 ASP cc_start: 0.8103 (t0) cc_final: 0.7771 (t70) outliers start: 4 outliers final: 4 residues processed: 117 average time/residue: 0.5638 time to fit residues: 70.1529 Evaluate side-chains 106 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 LYS 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: 0.9990 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.187982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115252 restraints weight = 7504.326| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.85 r_work: 0.3195 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8376 Z= 0.162 Angle : 0.469 4.950 11340 Z= 0.265 Chirality : 0.039 0.137 1248 Planarity : 0.004 0.031 1372 Dihedral : 3.879 15.252 1120 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.27 % Allowed : 12.56 % Favored : 85.17 % 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: 2.16 (0.26), residues: 984 helix: 1.50 (0.18), residues: 812 sheet: None (None), residues: 0 loop : 1.53 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 165 TYR 0.010 0.001 TYR C 74 PHE 0.012 0.002 PHE A 316 TRP 0.014 0.001 TRP B 270 HIS 0.004 0.002 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 8376) covalent geometry : angle 0.46893 / 0.26 (11340) hydrogen bonds : bond 0.04754 / 3.03 ( 637) hydrogen bonds : angle 4.25042 / 3.14 ( 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 135 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.310 Fit side-chains REVERT: A 89 ARG cc_start: 0.6946 (mtm-85) cc_final: 0.6086 (ttp-110) REVERT: A 162 LYS cc_start: 0.7087 (ttmt) cc_final: 0.6786 (tttp) REVERT: A 262 ASP cc_start: 0.8146 (t0) cc_final: 0.7831 (t70) REVERT: B 89 ARG cc_start: 0.6947 (mtm-85) cc_final: 0.6096 (ttp-110) REVERT: B 162 LYS cc_start: 0.7089 (ttmt) cc_final: 0.6784 (tttp) REVERT: B 262 ASP cc_start: 0.8139 (t0) cc_final: 0.7824 (t70) REVERT: C 89 ARG cc_start: 0.6942 (mtm-85) cc_final: 0.6085 (ttp-110) REVERT: C 162 LYS cc_start: 0.7102 (ttmt) cc_final: 0.6797 (tttp) REVERT: C 262 ASP cc_start: 0.8145 (t0) cc_final: 0.7829 (t70) REVERT: D 89 ARG cc_start: 0.6936 (mtm-85) cc_final: 0.6084 (ttp-110) REVERT: D 162 LYS cc_start: 0.7108 (ttmt) cc_final: 0.6802 (tttp) REVERT: D 262 ASP cc_start: 0.8151 (t0) cc_final: 0.7836 (t70) outliers start: 19 outliers final: 13 residues processed: 124 average time/residue: 0.6409 time to fit residues: 83.8595 Evaluate side-chains 117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 134 ILE 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 134 ILE 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: 0.8980 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.188687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116634 restraints weight = 7666.682| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.87 r_work: 0.3205 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1837 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= 0.140 Angle : 0.444 4.882 11340 Z= 0.251 Chirality : 0.038 0.141 1248 Planarity : 0.003 0.035 1372 Dihedral : 3.788 14.116 1120 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 2.27 % Allowed : 14.47 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.96 (0.26), residues: 984 helix: 1.86 (0.18), residues: 776 sheet: None (None), residues: 0 loop : 2.80 (0.49), residues: 208 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 A 137 TRP 0.012 0.001 TRP D 270 HIS 0.004 0.001 HIS C 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 8376) covalent geometry : angle 0.44428 / 0.25 (11340) hydrogen bonds : bond 0.04371 / 2.78 ( 637) hydrogen bonds : angle 4.14766 / 3.07 ( 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 : 0.267 Fit side-chains REVERT: A 89 ARG cc_start: 0.6987 (mtm-85) cc_final: 0.6142 (ttp-110) REVERT: A 121 SER cc_start: 0.7126 (OUTLIER) cc_final: 0.6881 (p) REVERT: A 162 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6734 (tttp) REVERT: A 262 ASP cc_start: 0.8068 (t0) cc_final: 0.7740 (t70) REVERT: B 89 ARG cc_start: 0.7007 (mtm-85) cc_final: 0.6155 (ttp-110) REVERT: B 121 SER cc_start: 0.7134 (OUTLIER) cc_final: 0.6881 (p) REVERT: B 162 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6733 (tttp) REVERT: B 262 ASP cc_start: 0.8065 (t0) cc_final: 0.7737 (t70) REVERT: C 89 ARG cc_start: 0.7001 (mtm-85) cc_final: 0.6180 (ttp-110) REVERT: C 121 SER cc_start: 0.7130 (OUTLIER) cc_final: 0.6885 (p) REVERT: C 162 LYS cc_start: 0.7004 (ttmt) cc_final: 0.6724 (tttp) REVERT: C 262 ASP cc_start: 0.8068 (t0) cc_final: 0.7737 (t70) REVERT: D 89 ARG cc_start: 0.6995 (mtm-85) cc_final: 0.6142 (ttp-110) REVERT: D 121 SER cc_start: 0.7123 (OUTLIER) cc_final: 0.6878 (p) REVERT: D 162 LYS cc_start: 0.7005 (ttmt) cc_final: 0.6725 (tttp) REVERT: D 262 ASP cc_start: 0.8070 (t0) cc_final: 0.7740 (t70) outliers start: 19 outliers final: 6 residues processed: 128 average time/residue: 0.6986 time to fit residues: 93.9310 Evaluate side-chains 127 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 134 ILE 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 134 ILE 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: 0.7980 chunk 4 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.188623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116795 restraints weight = 7594.057| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.87 r_work: 0.3216 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1980 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= 0.135 Angle : 0.430 4.870 11340 Z= 0.245 Chirality : 0.037 0.130 1248 Planarity : 0.003 0.037 1372 Dihedral : 3.760 14.051 1120 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.51 % Allowed : 13.88 % Favored : 83.61 % 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: 3.05 (0.27), residues: 984 helix: 1.88 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 3.03 (0.50), 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 0.009 0.001 PHE C 137 TRP 0.012 0.001 TRP D 270 HIS 0.004 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 8376) covalent geometry : angle 0.42976 / 0.25 (11340) hydrogen bonds : bond 0.04287 / 2.73 ( 637) hydrogen bonds : angle 4.08958 / 3.02 ( 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 123 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.328 Fit side-chains REVERT: A 89 ARG cc_start: 0.6992 (mtm-85) cc_final: 0.6138 (ttp-110) REVERT: A 121 SER cc_start: 0.7138 (OUTLIER) cc_final: 0.6913 (p) REVERT: A 162 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6725 (tttp) REVERT: A 262 ASP cc_start: 0.8204 (t0) cc_final: 0.7867 (t70) REVERT: B 89 ARG cc_start: 0.6999 (mtm-85) cc_final: 0.6141 (ttp-110) REVERT: B 121 SER cc_start: 0.7154 (OUTLIER) cc_final: 0.6921 (p) REVERT: B 162 LYS cc_start: 0.7017 (OUTLIER) cc_final: 0.6727 (tttp) REVERT: B 262 ASP cc_start: 0.8164 (t0) cc_final: 0.7820 (t70) REVERT: C 89 ARG cc_start: 0.7002 (mtm-85) cc_final: 0.6144 (ttp-110) REVERT: C 121 SER cc_start: 0.7153 (OUTLIER) cc_final: 0.6926 (p) REVERT: C 162 LYS cc_start: 0.7009 (OUTLIER) cc_final: 0.6723 (tttp) REVERT: C 262 ASP cc_start: 0.8196 (t0) cc_final: 0.7855 (t70) REVERT: D 89 ARG cc_start: 0.6992 (mtm-85) cc_final: 0.6134 (ttp-110) REVERT: D 121 SER cc_start: 0.7140 (OUTLIER) cc_final: 0.6914 (p) REVERT: D 162 LYS cc_start: 0.7007 (ttmt) cc_final: 0.6719 (tttp) REVERT: D 262 ASP cc_start: 0.8205 (t0) cc_final: 0.7871 (t70) outliers start: 21 outliers final: 6 residues processed: 116 average time/residue: 0.6487 time to fit residues: 79.5873 Evaluate side-chains 115 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 134 ILE 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 134 ILE Chi-restraints excluded: chain C residue 162 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4110 r_free = 0.4110 target = 0.188406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116887 restraints weight = 7529.717| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.86 r_work: 0.3218 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2020 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= 0.132 Angle : 0.427 4.866 11340 Z= 0.242 Chirality : 0.037 0.128 1248 Planarity : 0.003 0.037 1372 Dihedral : 3.724 13.890 1120 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.87 % Allowed : 13.52 % Favored : 83.61 % 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: 3.14 (0.27), residues: 984 helix: 1.94 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 3.09 (0.51), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 165 TYR 0.010 0.001 TYR A 74 PHE 0.009 0.001 PHE C 137 TRP 0.012 0.001 TRP A 270 HIS 0.004 0.001 HIS C 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8376) covalent geometry : angle 0.42673 / 0.24 (11340) hydrogen bonds : bond 0.04209 / 2.68 ( 637) hydrogen bonds : angle 4.05234 / 2.99 ( 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 134 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.317 Fit side-chains REVERT: A 89 ARG cc_start: 0.7012 (mtm-85) cc_final: 0.6150 (ttp-110) REVERT: A 121 SER cc_start: 0.7121 (OUTLIER) cc_final: 0.6912 (p) REVERT: A 162 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6742 (tttp) REVERT: A 262 ASP cc_start: 0.8205 (t0) cc_final: 0.7877 (t70) REVERT: B 89 ARG cc_start: 0.7020 (mtm-85) cc_final: 0.6152 (ttp-110) REVERT: B 121 SER cc_start: 0.7147 (OUTLIER) cc_final: 0.6940 (p) REVERT: B 162 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6735 (tttp) REVERT: B 262 ASP cc_start: 0.8198 (t0) cc_final: 0.7872 (t70) REVERT: C 89 ARG cc_start: 0.7026 (mtm-85) cc_final: 0.6157 (ttp-110) REVERT: C 121 SER cc_start: 0.7139 (OUTLIER) cc_final: 0.6927 (p) REVERT: C 162 LYS cc_start: 0.7025 (ttmt) cc_final: 0.6742 (tttp) REVERT: C 262 ASP cc_start: 0.8199 (t0) cc_final: 0.7868 (t70) REVERT: D 89 ARG cc_start: 0.7014 (mtm-85) cc_final: 0.6146 (ttp-110) REVERT: D 121 SER cc_start: 0.7128 (OUTLIER) cc_final: 0.6917 (p) REVERT: D 162 LYS cc_start: 0.7010 (ttmt) cc_final: 0.6734 (tttp) REVERT: D 262 ASP cc_start: 0.8205 (t0) cc_final: 0.7876 (t70) outliers start: 24 outliers final: 10 residues processed: 124 average time/residue: 0.5958 time to fit residues: 78.3774 Evaluate side-chains 114 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 134 ILE Chi-restraints excluded: chain B residue 162 LYS 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 134 ILE 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: 0.6980 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 0.0270 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.189653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.118770 restraints weight = 7670.661| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.88 r_work: 0.3236 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8376 Z= 0.114 Angle : 0.408 4.846 11340 Z= 0.232 Chirality : 0.037 0.148 1248 Planarity : 0.003 0.037 1372 Dihedral : 3.646 13.006 1120 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.79 % Allowed : 15.55 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.27 (0.27), residues: 984 helix: 2.05 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 3.05 (0.50), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 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 B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 8376) covalent geometry : angle 0.40800 / 0.23 (11340) hydrogen bonds : bond 0.04020 / 2.56 ( 637) hydrogen bonds : angle 3.97053 / 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 119 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.244 Fit side-chains REVERT: A 89 ARG cc_start: 0.6982 (mtm-85) cc_final: 0.6155 (ttp-110) REVERT: A 162 LYS cc_start: 0.6998 (ttmt) cc_final: 0.6722 (tttp) REVERT: A 262 ASP cc_start: 0.8195 (t0) cc_final: 0.7850 (t70) REVERT: B 89 ARG cc_start: 0.6992 (mtm-85) cc_final: 0.6130 (ttp-110) REVERT: B 153 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6606 (mtm110) REVERT: B 162 LYS cc_start: 0.6991 (ttmt) cc_final: 0.6716 (tttp) REVERT: B 262 ASP cc_start: 0.8196 (t0) cc_final: 0.7852 (t70) REVERT: C 89 ARG cc_start: 0.7000 (mtm-85) cc_final: 0.6133 (ttp-110) REVERT: C 162 LYS cc_start: 0.6995 (ttmt) cc_final: 0.6722 (tttp) REVERT: C 262 ASP cc_start: 0.8201 (t0) cc_final: 0.7854 (t70) REVERT: D 89 ARG cc_start: 0.6985 (mtm-85) cc_final: 0.6154 (ttp-110) REVERT: D 162 LYS cc_start: 0.6989 (ttmt) cc_final: 0.6722 (tttp) REVERT: D 262 ASP cc_start: 0.8195 (t0) cc_final: 0.7844 (t70) outliers start: 15 outliers final: 10 residues processed: 115 average time/residue: 0.6762 time to fit residues: 81.9476 Evaluate side-chains 110 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE 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 C residue 134 ILE Chi-restraints excluded: chain C residue 260 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 47 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 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 = 0.4113 r_free = 0.4113 target = 0.188749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.117665 restraints weight = 7592.589| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.86 r_work: 0.3223 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8376 Z= 0.124 Angle : 0.415 4.858 11340 Z= 0.237 Chirality : 0.037 0.145 1248 Planarity : 0.003 0.038 1372 Dihedral : 3.684 13.632 1120 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.56 % Allowed : 15.79 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.23 (0.27), residues: 984 helix: 2.02 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 3.04 (0.50), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 165 TYR 0.009 0.001 TYR A 74 PHE 0.009 0.001 PHE A 137 TRP 0.011 0.001 TRP A 270 HIS 0.004 0.001 HIS C 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 8376) covalent geometry : angle 0.41456 / 0.24 (11340) hydrogen bonds : bond 0.04096 / 2.60 ( 637) hydrogen bonds : angle 3.99691 / 2.95 ( 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 123 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.401 Fit side-chains REVERT: A 89 ARG cc_start: 0.6912 (mtm-85) cc_final: 0.6105 (ttp-110) REVERT: A 162 LYS cc_start: 0.7040 (ttmt) cc_final: 0.6746 (tttp) REVERT: A 262 ASP cc_start: 0.8214 (t0) cc_final: 0.7879 (t70) REVERT: B 89 ARG cc_start: 0.6918 (mtm-85) cc_final: 0.6110 (ttp-110) REVERT: B 162 LYS cc_start: 0.7038 (ttmt) cc_final: 0.6769 (tttp) REVERT: B 262 ASP cc_start: 0.8211 (t0) cc_final: 0.7875 (t70) REVERT: C 89 ARG cc_start: 0.6974 (mtm-85) cc_final: 0.6135 (ttp-110) REVERT: C 162 LYS cc_start: 0.7042 (ttmt) cc_final: 0.6752 (tttp) REVERT: C 262 ASP cc_start: 0.8211 (t0) cc_final: 0.7872 (t70) REVERT: D 89 ARG cc_start: 0.6917 (mtm-85) cc_final: 0.6108 (ttp-110) REVERT: D 162 LYS cc_start: 0.7032 (ttmt) cc_final: 0.6748 (tttp) REVERT: D 262 ASP cc_start: 0.8213 (t0) cc_final: 0.7875 (t70) outliers start: 13 outliers final: 7 residues processed: 119 average time/residue: 0.6394 time to fit residues: 80.5015 Evaluate side-chains 112 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain B residue 134 ILE 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 D residue 260 HIS 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: 0.9990 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 96 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.188999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118086 restraints weight = 7625.297| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.87 r_work: 0.3233 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2204 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= 0.120 Angle : 0.410 4.856 11340 Z= 0.234 Chirality : 0.037 0.141 1248 Planarity : 0.003 0.038 1372 Dihedral : 3.664 13.364 1120 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 1.08 % Allowed : 16.27 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.26 (0.27), residues: 984 helix: 2.05 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 3.04 (0.50), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 165 TYR 0.009 0.001 TYR D 74 PHE 0.008 0.001 PHE C 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 0.00256 / 0.12 ( 8376) covalent geometry : angle 0.41018 / 0.23 (11340) hydrogen bonds : bond 0.04038 / 2.57 ( 637) hydrogen bonds : angle 3.97981 / 2.94 ( 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 110 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.385 Fit side-chains REVERT: A 89 ARG cc_start: 0.6923 (mtm-85) cc_final: 0.6113 (ttp-110) REVERT: A 162 LYS cc_start: 0.7099 (ttmt) cc_final: 0.6851 (tttp) REVERT: A 262 ASP cc_start: 0.8209 (t0) cc_final: 0.7871 (t70) REVERT: B 89 ARG cc_start: 0.6930 (mtm-85) cc_final: 0.6123 (ttp-110) REVERT: B 162 LYS cc_start: 0.7048 (ttmt) cc_final: 0.6757 (tttp) REVERT: B 262 ASP cc_start: 0.8203 (t0) cc_final: 0.7866 (t70) REVERT: C 89 ARG cc_start: 0.6935 (mtm-85) cc_final: 0.6127 (ttp-110) REVERT: C 162 LYS cc_start: 0.7084 (ttmt) cc_final: 0.6840 (tttp) REVERT: C 262 ASP cc_start: 0.8205 (t0) cc_final: 0.7863 (t70) REVERT: D 89 ARG cc_start: 0.6929 (mtm-85) cc_final: 0.6118 (ttp-110) REVERT: D 162 LYS cc_start: 0.7064 (ttmt) cc_final: 0.6834 (tttp) REVERT: D 262 ASP cc_start: 0.8208 (t0) cc_final: 0.7868 (t70) outliers start: 9 outliers final: 5 residues processed: 106 average time/residue: 0.6504 time to fit residues: 72.9333 Evaluate side-chains 105 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 HIS 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 78 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 38 optimal weight: 0.0020 chunk 61 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 83 optimal weight: 0.2980 chunk 9 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 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 = 0.4132 r_free = 0.4132 target = 0.190848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120690 restraints weight = 7656.666| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.87 r_work: 0.3266 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 8376 Z= 0.103 Angle : 0.392 4.823 11340 Z= 0.224 Chirality : 0.036 0.137 1248 Planarity : 0.003 0.038 1372 Dihedral : 3.575 12.199 1120 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.60 % Allowed : 16.63 % 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: 3.45 (0.27), residues: 984 helix: 2.20 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 2.99 (0.50), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 165 TYR 0.009 0.001 TYR A 74 PHE 0.008 0.001 PHE D 137 TRP 0.010 0.001 TRP C 270 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 ( 8376) covalent geometry : angle 0.39230 / 0.22 (11340) hydrogen bonds : bond 0.03806 / 2.41 ( 637) hydrogen bonds : angle 3.86601 / 2.86 ( 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 106 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.367 Fit side-chains REVERT: A 89 ARG cc_start: 0.7095 (mtm-85) cc_final: 0.6283 (ttp-110) REVERT: A 162 LYS cc_start: 0.7017 (ttmt) cc_final: 0.6744 (tttp) REVERT: A 262 ASP cc_start: 0.8120 (t0) cc_final: 0.7161 (m-30) REVERT: B 89 ARG cc_start: 0.7106 (mtm-85) cc_final: 0.6292 (ttp-110) REVERT: B 162 LYS cc_start: 0.7084 (ttmt) cc_final: 0.6811 (tttp) REVERT: B 262 ASP cc_start: 0.8115 (t0) cc_final: 0.7154 (m-30) REVERT: C 89 ARG cc_start: 0.7105 (mtm-85) cc_final: 0.6295 (ttp-110) REVERT: C 162 LYS cc_start: 0.7016 (ttmt) cc_final: 0.6739 (tttp) REVERT: C 262 ASP cc_start: 0.8120 (t0) cc_final: 0.7156 (m-30) REVERT: D 89 ARG cc_start: 0.7106 (mtm-85) cc_final: 0.6291 (ttp-110) REVERT: D 162 LYS cc_start: 0.6984 (ttmt) cc_final: 0.6708 (tttp) REVERT: D 262 ASP cc_start: 0.8118 (t0) cc_final: 0.7156 (m-30) outliers start: 5 outliers final: 1 residues processed: 105 average time/residue: 0.6734 time to fit residues: 74.6061 Evaluate side-chains 95 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 134 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 70 optimal weight: 0.0870 chunk 56 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.189798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.119121 restraints weight = 7648.925| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.87 r_work: 0.3243 rms_B_bonded: 2.52 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: 0.7227 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8376 Z= 0.111 Angle : 0.400 4.836 11340 Z= 0.228 Chirality : 0.036 0.135 1248 Planarity : 0.003 0.038 1372 Dihedral : 3.602 13.032 1120 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 0.48 % Allowed : 16.63 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.42 (0.26), residues: 984 helix: 2.16 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 3.08 (0.51), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 165 TYR 0.009 0.001 TYR A 74 PHE 0.009 0.001 PHE D 137 TRP 0.011 0.001 TRP C 270 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 8376) covalent geometry : angle 0.39980 / 0.23 (11340) hydrogen bonds : bond 0.03932 / 2.50 ( 637) hydrogen bonds : angle 3.89465 / 2.88 ( 1839) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5190.92 seconds wall clock time: 88 minutes 50.94 seconds (5330.94 seconds total)