Starting phenix.real_space_refine on Fri Jul 3 23:13:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d1g_27129/07_2026/8d1g_27129_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1g_27129/07_2026/8d1g_27129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d1g_27129/07_2026/8d1g_27129_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1g_27129/07_2026/8d1g_27129_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d1g_27129/07_2026/8d1g_27129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1g_27129/07_2026/8d1g_27129.map" } resolution = 2.07 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= -0.002 sd= 0.130 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: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 P 15 5.49 5 S 80 5.16 5 Cl 1 4.86 5 C 10490 2.51 5 N 2355 2.21 5 O 3255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s 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: 16201 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2931 Chain: "B" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2931 Chain: "E" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2931 Chain: "C" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2931 Chain: "D" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2931 Chain: "A" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 245 Ad-hoc single atom residues: {' CA': 1, ' CL': 1} Unusual residues: {'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain breaks: 2 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 245 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain breaks: 1 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 48 Chain: "E" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 245 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 11} Link IDs: {None: 9} Chain breaks: 1 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 245 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain breaks: 1 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 245 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 11} Link IDs: {None: 9} Chain breaks: 1 Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-1': 7, 'MC3:plan-2': 7} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "E" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "C" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "D" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Time building chain proxies: 5.28, per 1000 atoms: 0.33 Number of scatterers: 16201 At special positions: 0 Unit cell: (90.47, 92.13, 110.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 5 19.99 Cl 1 17.00 S 80 16.00 P 15 15.00 O 3255 8.00 N 2355 7.00 C 10490 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 954.0 milliseconds 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 0 sheets defined 76.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 17 through 23 removed outlier: 3.594A pdb=" N LEU A 22 " --> pdb=" O GLN A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.608A pdb=" N ARG A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 73 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 99 Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 118 through 144 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 296 removed outlier: 4.498A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 17 through 23 removed outlier: 3.593A pdb=" N LEU B 22 " --> pdb=" O GLN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.608A pdb=" N ARG B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 73 Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 99 Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 118 through 144 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 182 through 198 Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 296 removed outlier: 4.498A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 323 Processing helix chain 'E' and resid 6 through 10 Processing helix chain 'E' and resid 17 through 23 removed outlier: 3.594A pdb=" N LEU E 22 " --> pdb=" O GLN E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 53 removed outlier: 5.608A pdb=" N ARG E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 99 Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 182 through 198 Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 296 removed outlier: 4.497A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 323 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.594A pdb=" N LEU C 22 " --> pdb=" O GLN C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 53 removed outlier: 5.608A pdb=" N ARG C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 73 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 77 through 99 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 296 removed outlier: 4.498A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 323 Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 17 through 23 removed outlier: 3.594A pdb=" N LEU D 22 " --> pdb=" O GLN D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.607A pdb=" N ARG D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 77 through 99 Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 118 through 144 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 182 through 198 Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 296 removed outlier: 4.497A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 323 980 hydrogen bonds defined for protein. 2830 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: 2.65 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2240 1.32 - 1.44: 4570 1.44 - 1.56: 8985 1.56 - 1.69: 30 1.69 - 1.81: 120 Bond restraints: 15945 Sorted by residual: bond pdb=" N VAL D 81 " pdb=" CA VAL D 81 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.18e+00 bond pdb=" N VAL C 81 " pdb=" CA VAL C 81 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.90e+00 bond pdb=" N VAL A 81 " pdb=" CA VAL A 81 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.86e+00 bond pdb=" N VAL B 81 " pdb=" CA VAL B 81 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.83e+00 bond pdb=" N VAL E 81 " pdb=" CA VAL E 81 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.58e+00 ... (remaining 15940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 20994 2.19 - 4.38: 346 4.38 - 6.58: 20 6.58 - 8.77: 5 8.77 - 10.96: 10 Bond angle restraints: 21375 Sorted by residual: angle pdb=" O3P MC3 E 505 " pdb=" P MC3 E 505 " pdb=" O4P MC3 E 505 " ideal model delta sigma weight residual 93.26 104.22 -10.96 3.00e+00 1.11e-01 1.33e+01 angle pdb=" O3P MC3 A 504 " pdb=" P MC3 A 504 " pdb=" O4P MC3 A 504 " ideal model delta sigma weight residual 93.26 104.22 -10.96 3.00e+00 1.11e-01 1.33e+01 angle pdb=" O3P MC3 B 504 " pdb=" P MC3 B 504 " pdb=" O4P MC3 B 504 " ideal model delta sigma weight residual 93.26 104.20 -10.94 3.00e+00 1.11e-01 1.33e+01 angle pdb=" O3P MC3 C 504 " pdb=" P MC3 C 504 " pdb=" O4P MC3 C 504 " ideal model delta sigma weight residual 93.26 104.20 -10.94 3.00e+00 1.11e-01 1.33e+01 angle pdb=" O3P MC3 D 505 " pdb=" P MC3 D 505 " pdb=" O4P MC3 D 505 " ideal model delta sigma weight residual 93.26 104.20 -10.94 3.00e+00 1.11e-01 1.33e+01 ... (remaining 21370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.46: 8848 27.46 - 54.91: 807 54.91 - 82.37: 140 82.37 - 109.83: 30 109.83 - 137.28: 10 Dihedral angle restraints: 9835 sinusoidal: 4685 harmonic: 5150 Sorted by residual: dihedral pdb=" C33 MC3 D 505 " pdb=" C31 MC3 D 505 " pdb=" C32 MC3 D 505 " pdb=" O2 MC3 D 505 " ideal model delta sinusoidal sigma weight residual 175.52 -47.20 -137.28 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C33 MC3 C 504 " pdb=" C31 MC3 C 504 " pdb=" C32 MC3 C 504 " pdb=" O2 MC3 C 504 " ideal model delta sinusoidal sigma weight residual 175.52 -47.20 -137.28 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C33 MC3 A 504 " pdb=" C31 MC3 A 504 " pdb=" C32 MC3 A 504 " pdb=" O2 MC3 A 504 " ideal model delta sinusoidal sigma weight residual 175.52 -47.22 -137.26 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 9832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1453 0.034 - 0.067: 590 0.067 - 0.101: 141 0.101 - 0.135: 46 0.135 - 0.168: 15 Chirality restraints: 2245 Sorted by residual: chirality pdb=" CA VAL B 232 " pdb=" N VAL B 232 " pdb=" C VAL B 232 " pdb=" CB VAL B 232 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CA VAL D 232 " pdb=" N VAL D 232 " pdb=" C VAL D 232 " pdb=" CB VAL D 232 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA VAL A 232 " pdb=" N VAL A 232 " pdb=" C VAL A 232 " pdb=" CB VAL A 232 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 2242 not shown) Planarity restraints: 2530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 282 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C PHE E 282 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE E 282 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE E 283 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 282 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C PHE D 282 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE D 282 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE D 283 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 282 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C PHE B 282 " 0.028 2.00e-02 2.50e+03 pdb=" O PHE B 282 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE B 283 " -0.009 2.00e-02 2.50e+03 ... (remaining 2527 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1879 2.75 - 3.28: 16364 3.28 - 3.82: 31540 3.82 - 4.36: 38590 4.36 - 4.90: 60758 Nonbonded interactions: 149131 Sorted by model distance: nonbonded pdb=" O HOH B 655 " pdb=" O HOH C 704 " model vdw 2.207 3.040 nonbonded pdb=" O HOH A 704 " pdb=" O HOH E 655 " model vdw 2.215 3.040 nonbonded pdb=" O HOH A 655 " pdb=" O HOH B 704 " model vdw 2.215 3.040 nonbonded pdb=" O HOH E 704 " pdb=" O HOH D 656 " model vdw 2.219 3.040 nonbonded pdb=" O HOH C 655 " pdb=" O HOH D 704 " model vdw 2.226 3.040 ... (remaining 149126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 365 or resid 504 through 507 or (resid 508 and (name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or na \ me C42 or name C43 or name C44)) or resid 509 through 511 or (resid 512 and (nam \ e C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or \ name C44)))) selection = (chain 'B' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 365 or resid 504 through 507 or (resid 508 and (name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or na \ me C42 or name C43 or name C44)) or resid 509 through 511 or (resid 512 and (nam \ e C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or \ name C44)))) selection = (chain 'C' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 365 or resid 504 through 507 or (resid 508 and (name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or na \ me C42 or name C43 or name C44)) or resid 509 through 511 or (resid 512 and (nam \ e C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or \ name C44)))) selection = (chain 'D' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 365 or resid 504 or (resid 505 through 506 and (name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or na \ me C40 or name C41 or name C42 or name C43 or name C44)) or (resid 507 through 5 \ 08 and (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name C40 or name C41 or name C42 or name C43 or name C44)) or resid \ 509 or (resid 510 and (name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name \ C44)) or (resid 511 through 512 and (name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'E' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 365 or resid 504 or (resid 505 through 506 and (name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or na \ me C40 or name C41 or name C42 or name C43 or name C44)) or (resid 507 through 5 \ 08 and (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name C40 or name C41 or name C42 or name C43 or name C44)) or resid \ 509 or (resid 510 and (name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name \ C44)) or (resid 511 through 512 and (name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43 or name C44)))) } 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=0.50 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: 6.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 17.000 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 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 : 0.006 0.050 15945 Z= 0.318 Angle : 0.690 10.959 21375 Z= 0.368 Chirality : 0.041 0.168 2245 Planarity : 0.003 0.018 2530 Dihedral : 20.598 137.282 6535 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.66 % Allowed : 12.46 % Favored : 86.89 % 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: 1.81 (0.20), residues: 1715 helix: 1.80 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : -0.14 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 313 TYR 0.024 0.002 TYR B 97 PHE 0.020 0.002 PHE E 248 TRP 0.015 0.002 TRP B 338 HIS 0.004 0.001 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.32 (15945) covalent geometry : angle 0.69048 / 0.37 (21375) hydrogen bonds : bond 0.14084 / 9.45 ( 980) hydrogen bonds : angle 4.95382 / 3.65 ( 2830) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7231 (ptp90) cc_final: 0.6794 (mtt180) REVERT: E 13 ARG cc_start: 0.7072 (ptp90) cc_final: 0.6777 (mpt180) REVERT: C 13 ARG cc_start: 0.7230 (ptp90) cc_final: 0.6845 (mpt180) REVERT: C 159 GLU cc_start: 0.7370 (mp0) cc_final: 0.6981 (mm-30) REVERT: D 13 ARG cc_start: 0.7324 (ptp90) cc_final: 0.6928 (mtt90) REVERT: D 44 MET cc_start: 0.8753 (mmt) cc_final: 0.8448 (mmm) REVERT: D 71 GLN cc_start: 0.7831 (tt0) cc_final: 0.7630 (tt0) REVERT: D 333 GLU cc_start: 0.7205 (tt0) cc_final: 0.6901 (pm20) outliers start: 10 outliers final: 3 residues processed: 218 average time/residue: 0.6752 time to fit residues: 159.9328 Evaluate side-chains 179 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 303 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 ASN A 316 GLN B 173 ASN B 175 ASN B 316 GLN E 173 ASN E 175 ASN E 316 GLN C 175 ASN C 316 GLN D 19 GLN D 316 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.138382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108062 restraints weight = 33576.081| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.53 r_work: 0.3204 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15945 Z= 0.168 Angle : 0.564 6.572 21375 Z= 0.307 Chirality : 0.039 0.171 2245 Planarity : 0.004 0.032 2530 Dihedral : 17.826 116.620 3273 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.18 % Allowed : 10.36 % Favored : 88.46 % 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: 1.81 (0.20), residues: 1715 helix: 1.72 (0.14), residues: 1245 sheet: None (None), residues: 0 loop : -0.10 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 13 TYR 0.023 0.002 TYR C 97 PHE 0.021 0.002 PHE E 248 TRP 0.015 0.002 TRP C 94 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (15945) covalent geometry : angle 0.56352 / 0.31 (21375) hydrogen bonds : bond 0.07091 / 4.74 ( 980) hydrogen bonds : angle 4.65847 / 3.46 ( 2830) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7116 (ptp90) cc_final: 0.6325 (mtt180) REVERT: A 327 ASP cc_start: 0.8550 (t0) cc_final: 0.8165 (t70) REVERT: B 19 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7559 (pm20) REVERT: B 168 ARG cc_start: 0.8609 (tmt90) cc_final: 0.8381 (tmt90) REVERT: B 172 GLU cc_start: 0.8287 (mm-30) cc_final: 0.6768 (mp0) REVERT: E 13 ARG cc_start: 0.7094 (ptp90) cc_final: 0.6413 (mtt90) REVERT: E 19 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.6810 (pm20) REVERT: E 78 VAL cc_start: 0.7958 (p) cc_final: 0.7687 (t) REVERT: E 159 GLU cc_start: 0.7447 (pp20) cc_final: 0.7177 (pp20) REVERT: C 13 ARG cc_start: 0.7285 (ptp90) cc_final: 0.6504 (mpt180) REVERT: C 19 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7138 (pp30) REVERT: C 159 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: C 168 ARG cc_start: 0.8616 (tmt90) cc_final: 0.8365 (tmt90) REVERT: C 303 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.7694 (t0) REVERT: D 13 ARG cc_start: 0.7201 (ptp90) cc_final: 0.6621 (mtm-85) REVERT: D 44 MET cc_start: 0.8976 (mmt) cc_final: 0.8630 (mmm) REVERT: D 175 ASN cc_start: 0.8448 (m110) cc_final: 0.8113 (t0) REVERT: D 333 GLU cc_start: 0.7227 (tt0) cc_final: 0.6022 (pm20) outliers start: 18 outliers final: 7 residues processed: 218 average time/residue: 0.7031 time to fit residues: 167.7652 Evaluate side-chains 204 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 161 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 151 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.135913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105487 restraints weight = 34251.720| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.55 r_work: 0.3162 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15945 Z= 0.207 Angle : 0.590 5.362 21375 Z= 0.328 Chirality : 0.041 0.167 2245 Planarity : 0.005 0.037 2530 Dihedral : 16.455 110.457 3271 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.18 % Allowed : 10.36 % Favored : 88.46 % 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: 1.63 (0.20), residues: 1715 helix: 1.56 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : -0.08 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 313 TYR 0.027 0.003 TYR A 97 PHE 0.023 0.003 PHE C 248 TRP 0.014 0.002 TRP C 94 HIS 0.005 0.001 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (15945) covalent geometry : angle 0.59002 / 0.33 (21375) hydrogen bonds : bond 0.07807 / 5.22 ( 980) hydrogen bonds : angle 4.75283 / 3.54 ( 2830) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7095 (ptp90) cc_final: 0.6384 (mtt180) REVERT: A 36 LEU cc_start: 0.8713 (tp) cc_final: 0.8425 (tm) REVERT: A 175 ASN cc_start: 0.8405 (m110) cc_final: 0.8119 (t0) REVERT: B 19 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: E 13 ARG cc_start: 0.7131 (ptp90) cc_final: 0.6454 (mtt90) REVERT: E 19 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.6753 (pm20) REVERT: E 78 VAL cc_start: 0.8009 (OUTLIER) cc_final: 0.7789 (t) REVERT: E 159 GLU cc_start: 0.7512 (pp20) cc_final: 0.7270 (pp20) REVERT: E 253 ILE cc_start: 0.8176 (mm) cc_final: 0.7903 (mm) REVERT: C 13 ARG cc_start: 0.7260 (ptp90) cc_final: 0.6505 (mpt180) REVERT: C 19 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7211 (pp30) REVERT: C 168 ARG cc_start: 0.8560 (tmt90) cc_final: 0.8321 (tmt90) REVERT: C 303 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.7676 (t0) REVERT: C 325 MET cc_start: 0.9095 (mtp) cc_final: 0.8801 (mtp) REVERT: D 13 ARG cc_start: 0.7215 (ptp90) cc_final: 0.6645 (mtm-85) REVERT: D 19 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: D 44 MET cc_start: 0.9001 (mmt) cc_final: 0.8601 (mmm) REVERT: D 175 ASN cc_start: 0.8563 (m110) cc_final: 0.8178 (t0) REVERT: D 197 ARG cc_start: 0.8424 (ttm170) cc_final: 0.8047 (tpm170) REVERT: D 333 GLU cc_start: 0.7267 (tt0) cc_final: 0.5989 (pm20) outliers start: 18 outliers final: 8 residues processed: 208 average time/residue: 0.6569 time to fit residues: 149.2333 Evaluate side-chains 199 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 133 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 GLN B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.136716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106810 restraints weight = 31860.367| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.48 r_work: 0.3183 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15945 Z= 0.184 Angle : 0.554 5.848 21375 Z= 0.310 Chirality : 0.040 0.167 2245 Planarity : 0.004 0.038 2530 Dihedral : 15.711 106.399 3271 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.11 % Allowed : 10.16 % Favored : 88.72 % 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: 1.67 (0.20), residues: 1715 helix: 1.56 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : 0.01 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 165 TYR 0.026 0.002 TYR C 97 PHE 0.020 0.002 PHE C 248 TRP 0.014 0.002 TRP C 94 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (15945) covalent geometry : angle 0.55353 / 0.31 (21375) hydrogen bonds : bond 0.07407 / 4.94 ( 980) hydrogen bonds : angle 4.68087 / 3.49 ( 2830) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7098 (ptp90) cc_final: 0.6326 (mtt90) REVERT: A 36 LEU cc_start: 0.8727 (tp) cc_final: 0.8437 (tm) REVERT: A 175 ASN cc_start: 0.8349 (m110) cc_final: 0.8068 (t0) REVERT: A 324 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: B 172 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7845 (mm-30) REVERT: E 13 ARG cc_start: 0.7095 (ptp90) cc_final: 0.6519 (mtt90) REVERT: E 19 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.6767 (pm20) REVERT: E 78 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7781 (t) REVERT: E 159 GLU cc_start: 0.7493 (pp20) cc_final: 0.7250 (pp20) REVERT: E 172 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7834 (mm-30) REVERT: E 253 ILE cc_start: 0.8138 (mm) cc_final: 0.7876 (mm) REVERT: C 13 ARG cc_start: 0.7222 (ptp90) cc_final: 0.6492 (mpt180) REVERT: C 19 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7195 (pp30) REVERT: C 303 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7651 (t0) REVERT: D 13 ARG cc_start: 0.7205 (ptp90) cc_final: 0.6611 (mtm-85) REVERT: D 44 MET cc_start: 0.8997 (mmt) cc_final: 0.8595 (mmm) REVERT: D 175 ASN cc_start: 0.8559 (m110) cc_final: 0.8186 (t0) REVERT: D 197 ARG cc_start: 0.8371 (ttm170) cc_final: 0.8023 (tpm170) REVERT: D 293 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8096 (tm130) REVERT: D 333 GLU cc_start: 0.7235 (tt0) cc_final: 0.5978 (pm20) outliers start: 17 outliers final: 7 residues processed: 196 average time/residue: 0.7331 time to fit residues: 156.7794 Evaluate side-chains 197 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 75 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 145 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN D 19 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.136145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.105907 restraints weight = 34417.515| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.54 r_work: 0.3169 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15945 Z= 0.199 Angle : 0.574 6.530 21375 Z= 0.320 Chirality : 0.040 0.167 2245 Planarity : 0.005 0.040 2530 Dihedral : 15.416 103.833 3271 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.18 % Allowed : 10.03 % Favored : 88.79 % 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: 1.62 (0.20), residues: 1715 helix: 1.52 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : -0.00 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 218 TYR 0.027 0.002 TYR C 97 PHE 0.021 0.002 PHE C 248 TRP 0.013 0.002 TRP C 94 HIS 0.006 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (15945) covalent geometry : angle 0.57445 / 0.32 (21375) hydrogen bonds : bond 0.07676 / 5.13 ( 980) hydrogen bonds : angle 4.72172 / 3.52 ( 2830) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7074 (ptp90) cc_final: 0.6385 (mtt90) REVERT: A 36 LEU cc_start: 0.8752 (tp) cc_final: 0.8453 (tm) REVERT: A 175 ASN cc_start: 0.8353 (m110) cc_final: 0.8073 (t0) REVERT: A 324 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: B 19 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7463 (pm20) REVERT: E 13 ARG cc_start: 0.7072 (ptp90) cc_final: 0.6463 (mtt90) REVERT: E 19 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.6742 (pm20) REVERT: E 78 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7752 (t) REVERT: E 159 GLU cc_start: 0.7535 (pp20) cc_final: 0.7306 (pp20) REVERT: E 172 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7891 (mm-30) REVERT: E 253 ILE cc_start: 0.8164 (mm) cc_final: 0.7888 (mm) REVERT: C 13 ARG cc_start: 0.7286 (ptp90) cc_final: 0.6538 (mpt180) REVERT: C 19 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7201 (pp30) REVERT: C 303 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7622 (t0) REVERT: C 325 MET cc_start: 0.9045 (mtp) cc_final: 0.8828 (mtp) REVERT: D 13 ARG cc_start: 0.7157 (ptp90) cc_final: 0.6543 (mtm-85) REVERT: D 44 MET cc_start: 0.9012 (mmt) cc_final: 0.8601 (mmm) REVERT: D 197 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8018 (tpm170) REVERT: D 293 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8121 (tm130) REVERT: D 333 GLU cc_start: 0.7266 (tt0) cc_final: 0.6022 (pm20) outliers start: 18 outliers final: 10 residues processed: 198 average time/residue: 0.6964 time to fit residues: 150.9702 Evaluate side-chains 201 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 167 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 GLN B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN D 175 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107847 restraints weight = 29376.990| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.41 r_work: 0.3200 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15945 Z= 0.174 Angle : 0.541 6.686 21375 Z= 0.304 Chirality : 0.039 0.166 2245 Planarity : 0.004 0.041 2530 Dihedral : 15.023 101.869 3271 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.25 % Allowed : 10.03 % Favored : 88.72 % 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: 1.67 (0.20), residues: 1715 helix: 1.56 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : 0.00 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 13 TYR 0.024 0.002 TYR C 97 PHE 0.019 0.002 PHE C 248 TRP 0.013 0.002 TRP C 94 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (15945) covalent geometry : angle 0.54099 / 0.30 (21375) hydrogen bonds : bond 0.07282 / 4.85 ( 980) hydrogen bonds : angle 4.65256 / 3.47 ( 2830) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7069 (ptp90) cc_final: 0.6373 (mtt90) REVERT: A 36 LEU cc_start: 0.8756 (tp) cc_final: 0.8460 (tm) REVERT: A 175 ASN cc_start: 0.8323 (m110) cc_final: 0.8046 (t0) REVERT: A 324 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: E 13 ARG cc_start: 0.7084 (ptp90) cc_final: 0.6515 (mtt90) REVERT: E 19 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.6711 (pm20) REVERT: E 78 VAL cc_start: 0.7972 (OUTLIER) cc_final: 0.7719 (t) REVERT: E 159 GLU cc_start: 0.7510 (pp20) cc_final: 0.7285 (pp20) REVERT: E 172 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7792 (mm-30) REVERT: E 253 ILE cc_start: 0.8107 (mm) cc_final: 0.7847 (mm) REVERT: C 13 ARG cc_start: 0.7236 (ptp90) cc_final: 0.6527 (mpt180) REVERT: C 19 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: C 303 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.7587 (t0) REVERT: C 325 MET cc_start: 0.9042 (mtp) cc_final: 0.8825 (mtp) REVERT: D 13 ARG cc_start: 0.7124 (ptp90) cc_final: 0.6546 (mtm-85) REVERT: D 19 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.6980 (pm20) REVERT: D 44 MET cc_start: 0.8997 (mmt) cc_final: 0.8623 (mmm) REVERT: D 175 ASN cc_start: 0.8394 (m-40) cc_final: 0.8101 (t0) REVERT: D 197 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8006 (tpm170) REVERT: D 293 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8058 (tm130) REVERT: D 333 GLU cc_start: 0.7290 (tt0) cc_final: 0.6062 (pm20) outliers start: 19 outliers final: 9 residues processed: 196 average time/residue: 0.7600 time to fit residues: 162.6500 Evaluate side-chains 199 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 138 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN D 19 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.137061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107731 restraints weight = 29099.140| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.41 r_work: 0.3200 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (15 function evaluations) r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15945 Z= 0.177 Angle : 0.545 7.538 21375 Z= 0.306 Chirality : 0.039 0.165 2245 Planarity : 0.004 0.042 2530 Dihedral : 14.829 100.029 3271 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.18 % Allowed : 10.03 % Favored : 88.79 % 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: 1.67 (0.20), residues: 1715 helix: 1.56 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : 0.04 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 168 TYR 0.024 0.002 TYR C 97 PHE 0.019 0.002 PHE C 248 TRP 0.013 0.002 TRP C 94 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (15945) covalent geometry : angle 0.54539 / 0.31 (21375) hydrogen bonds : bond 0.07325 / 4.88 ( 980) hydrogen bonds : angle 4.65588 / 3.47 ( 2830) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7081 (ptp90) cc_final: 0.6376 (mtt90) REVERT: A 36 LEU cc_start: 0.8772 (tp) cc_final: 0.8481 (tm) REVERT: A 175 ASN cc_start: 0.8336 (m110) cc_final: 0.8065 (t0) REVERT: A 324 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: E 13 ARG cc_start: 0.7037 (ptp90) cc_final: 0.6483 (mtt90) REVERT: E 19 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.6729 (pm20) REVERT: E 71 GLN cc_start: 0.8094 (tt0) cc_final: 0.7857 (tt0) REVERT: E 78 VAL cc_start: 0.7970 (OUTLIER) cc_final: 0.7716 (t) REVERT: E 159 GLU cc_start: 0.7517 (pp20) cc_final: 0.7299 (pp20) REVERT: E 253 ILE cc_start: 0.8127 (mm) cc_final: 0.7869 (mm) REVERT: C 13 ARG cc_start: 0.7237 (ptp90) cc_final: 0.6540 (mpt180) REVERT: C 19 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: C 303 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7633 (t0) REVERT: C 325 MET cc_start: 0.9048 (mtp) cc_final: 0.8823 (mtp) REVERT: D 13 ARG cc_start: 0.7180 (ptp90) cc_final: 0.6514 (mtt90) REVERT: D 44 MET cc_start: 0.9006 (mmt) cc_final: 0.8640 (mmm) REVERT: D 175 ASN cc_start: 0.8395 (m-40) cc_final: 0.8109 (t0) REVERT: D 293 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8064 (tm130) REVERT: D 333 GLU cc_start: 0.7301 (tt0) cc_final: 0.6102 (pm20) outliers start: 18 outliers final: 10 residues processed: 192 average time/residue: 0.7232 time to fit residues: 151.8251 Evaluate side-chains 199 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 293 GLN Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 138 optimal weight: 0.1980 chunk 63 optimal weight: 0.0670 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 17 optimal weight: 0.0010 chunk 140 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.143068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113862 restraints weight = 37970.853| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.58 r_work: 0.3283 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15945 Z= 0.117 Angle : 0.458 7.067 21375 Z= 0.259 Chirality : 0.036 0.163 2245 Planarity : 0.003 0.040 2530 Dihedral : 13.960 96.451 3271 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.66 % Allowed : 10.56 % Favored : 88.79 % 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 (0.20), residues: 1715 helix: 1.74 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : -0.10 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 117 TYR 0.028 0.001 TYR B 236 PHE 0.021 0.002 PHE E 42 TRP 0.016 0.002 TRP E 94 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.12 (15945) covalent geometry : angle 0.45789 / 0.26 (21375) hydrogen bonds : bond 0.05780 / 3.84 ( 980) hydrogen bonds : angle 4.43382 / 3.30 ( 2830) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 201 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.6958 (ptp90) cc_final: 0.6032 (mpt180) REVERT: A 175 ASN cc_start: 0.8177 (m110) cc_final: 0.7893 (t0) REVERT: E 13 ARG cc_start: 0.7110 (ptp90) cc_final: 0.6483 (mpt180) REVERT: E 159 GLU cc_start: 0.7460 (pp20) cc_final: 0.7176 (pp20) REVERT: E 172 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7787 (mm-30) REVERT: C 13 ARG cc_start: 0.7193 (ptp90) cc_final: 0.6413 (mpt180) REVERT: C 19 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7622 (pm20) REVERT: C 325 MET cc_start: 0.9089 (mtp) cc_final: 0.8808 (mtp) REVERT: D 13 ARG cc_start: 0.7088 (ptp90) cc_final: 0.6516 (mtm-85) REVERT: D 19 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6739 (pm20) REVERT: D 44 MET cc_start: 0.8921 (mmt) cc_final: 0.8661 (mmm) REVERT: D 175 ASN cc_start: 0.8317 (m-40) cc_final: 0.8043 (t0) REVERT: D 197 ARG cc_start: 0.8310 (ttm170) cc_final: 0.8004 (tpm170) REVERT: D 333 GLU cc_start: 0.7370 (tt0) cc_final: 0.6157 (pm20) outliers start: 10 outliers final: 4 residues processed: 205 average time/residue: 0.6906 time to fit residues: 155.4087 Evaluate side-chains 192 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 186 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 43 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 GLN B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN D 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.139118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108769 restraints weight = 40673.034| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.64 r_work: 0.3208 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (11 function evaluations) r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15945 Z= 0.149 Angle : 0.506 8.128 21375 Z= 0.285 Chirality : 0.038 0.168 2245 Planarity : 0.004 0.044 2530 Dihedral : 13.900 92.312 3267 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.59 % Allowed : 11.21 % Favored : 88.20 % 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: 1.84 (0.20), residues: 1715 helix: 1.70 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : 0.02 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 13 TYR 0.031 0.002 TYR B 236 PHE 0.023 0.002 PHE E 42 TRP 0.013 0.002 TRP C 94 HIS 0.004 0.001 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (15945) covalent geometry : angle 0.50578 / 0.29 (21375) hydrogen bonds : bond 0.06654 / 4.44 ( 980) hydrogen bonds : angle 4.52974 / 3.38 ( 2830) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7040 (ptp90) cc_final: 0.6321 (mtt90) REVERT: A 175 ASN cc_start: 0.8250 (m110) cc_final: 0.7971 (t0) REVERT: B 172 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7120 (mp0) REVERT: E 13 ARG cc_start: 0.7094 (ptp90) cc_final: 0.6439 (mpt180) REVERT: E 159 GLU cc_start: 0.7467 (pp20) cc_final: 0.7248 (pp20) REVERT: E 172 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7802 (mm-30) REVERT: C 13 ARG cc_start: 0.7228 (ptp90) cc_final: 0.6443 (mpt180) REVERT: C 19 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: C 168 ARG cc_start: 0.8595 (tmt90) cc_final: 0.8388 (tmt90) REVERT: D 13 ARG cc_start: 0.7168 (ptp90) cc_final: 0.6542 (mtm-85) REVERT: D 44 MET cc_start: 0.8953 (mmt) cc_final: 0.8606 (mmm) REVERT: D 175 ASN cc_start: 0.8354 (m-40) cc_final: 0.8071 (t0) REVERT: D 197 ARG cc_start: 0.8328 (ttm170) cc_final: 0.8002 (tpm170) REVERT: D 333 GLU cc_start: 0.7377 (tt0) cc_final: 0.6128 (pm20) outliers start: 9 outliers final: 5 residues processed: 191 average time/residue: 0.7384 time to fit residues: 154.1970 Evaluate side-chains 192 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 186 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 chunk 14 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 GLN B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN D 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.138622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108309 restraints weight = 36634.273| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.58 r_work: 0.3205 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15945 Z= 0.156 Angle : 0.521 8.451 21375 Z= 0.292 Chirality : 0.038 0.166 2245 Planarity : 0.004 0.043 2530 Dihedral : 13.871 91.275 3267 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.46 % Allowed : 11.74 % Favored : 87.80 % 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: 1.80 (0.20), residues: 1715 helix: 1.67 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : 0.03 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 13 TYR 0.032 0.002 TYR B 236 PHE 0.023 0.002 PHE E 42 TRP 0.013 0.002 TRP C 94 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (15945) covalent geometry : angle 0.52076 / 0.29 (21375) hydrogen bonds : bond 0.06841 / 4.56 ( 980) hydrogen bonds : angle 4.56160 / 3.40 ( 2830) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7042 (ptp90) cc_final: 0.6331 (mtt90) REVERT: A 175 ASN cc_start: 0.8263 (m110) cc_final: 0.7994 (t0) REVERT: B 172 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7792 (mm-30) REVERT: E 13 ARG cc_start: 0.7096 (ptp90) cc_final: 0.6493 (mpt180) REVERT: E 159 GLU cc_start: 0.7479 (pp20) cc_final: 0.7197 (pp20) REVERT: E 172 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7790 (mm-30) REVERT: C 13 ARG cc_start: 0.7214 (ptp90) cc_final: 0.6443 (mpt180) REVERT: C 19 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: C 168 ARG cc_start: 0.8614 (tmt90) cc_final: 0.8408 (tmt90) REVERT: D 13 ARG cc_start: 0.7153 (ptp90) cc_final: 0.6527 (mtm-85) REVERT: D 44 MET cc_start: 0.8989 (mmt) cc_final: 0.8739 (mmm) REVERT: D 175 ASN cc_start: 0.8363 (m-40) cc_final: 0.8082 (t0) REVERT: D 333 GLU cc_start: 0.7380 (tt0) cc_final: 0.6142 (pm20) outliers start: 7 outliers final: 4 residues processed: 189 average time/residue: 0.7409 time to fit residues: 153.5441 Evaluate side-chains 190 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 185 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 30 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 173 ASN B 175 ASN E 19 GLN E 173 ASN E 175 ASN C 175 ASN D 19 GLN D 58 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.141521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.113899 restraints weight = 27577.499| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.31 r_work: 0.3304 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15945 Z= 0.140 Angle : 0.498 8.109 21375 Z= 0.280 Chirality : 0.037 0.163 2245 Planarity : 0.004 0.042 2530 Dihedral : 13.554 89.269 3267 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.59 % Allowed : 11.61 % Favored : 87.80 % 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: 1.84 (0.20), residues: 1715 helix: 1.70 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : 0.01 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 13 TYR 0.034 0.002 TYR B 236 PHE 0.023 0.002 PHE E 42 TRP 0.014 0.002 TRP C 94 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (15945) covalent geometry : angle 0.49782 / 0.28 (21375) hydrogen bonds : bond 0.06482 / 4.32 ( 980) hydrogen bonds : angle 4.50927 / 3.36 ( 2830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7070.44 seconds wall clock time: 121 minutes 9.50 seconds (7269.50 seconds total)