Starting phenix.real_space_refine on Wed Mar 4 22:15:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d1g_27129/03_2026/8d1g_27129_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d1g_27129/03_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_27129/03_2026/8d1g_27129_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d1g_27129/03_2026/8d1g_27129_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d1g_27129/03_2026/8d1g_27129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d1g_27129/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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, 247 Unusual residues: {' CA': 1, ' CL': 1, 'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} 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, 246 Unusual residues: {' CA': 1, 'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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, 246 Unusual residues: {' CA': 1, 'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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, 246 Unusual residues: {' CA': 1, 'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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, 246 Unusual residues: {' CA': 1, 'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} 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: 6.49, per 1000 atoms: 0.40 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: 1.37 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.37 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: 2.43 Time building geometry restraints manager: 1.78 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: 6.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.650 Find NCS groups from input model: 0.370 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: 0.000 Load rotamer database and sin/cos tables:7.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 covalent geometry : bond 0.00611 (15945) covalent geometry : angle 0.69048 (21375) hydrogen bonds : bond 0.14084 ( 980) hydrogen bonds : angle 4.95382 ( 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 : 0.546 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: 0.8091 time to fit residues: 190.5352 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 : 0.570 ------------------------------------------------------------------------------- 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: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 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: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3704 r_free = 0.3704 target = 0.137938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107493 restraints weight = 33518.191| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.54 r_work: 0.3196 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 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 = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1084 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= 0.168 Angle : 0.562 6.825 21375 Z= 0.306 Chirality : 0.039 0.168 2245 Planarity : 0.004 0.030 2530 Dihedral : 17.870 116.823 3273 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.18 % Allowed : 10.30 % Favored : 88.52 % 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: 1.86 (0.20), residues: 1715 helix: 1.76 (0.14), residues: 1245 sheet: None (None), residues: 0 loop : -0.07 (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 covalent geometry : bond 0.00330 (15945) covalent geometry : angle 0.56162 (21375) hydrogen bonds : bond 0.07158 ( 980) hydrogen bonds : angle 4.65166 ( 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 228 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 324 GLU cc_start: 0.8014 (mp0) cc_final: 0.7808 (mp0) REVERT: A 327 ASP cc_start: 0.8551 (t0) cc_final: 0.8166 (t70) REVERT: B 19 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7539 (pm20) REVERT: B 168 ARG cc_start: 0.8624 (tmt90) cc_final: 0.8401 (tmt90) REVERT: B 172 GLU cc_start: 0.8284 (mm-30) cc_final: 0.6766 (mp0) REVERT: E 13 ARG cc_start: 0.7134 (ptp90) cc_final: 0.6449 (mtt90) REVERT: E 19 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.6846 (pm20) REVERT: E 78 VAL cc_start: 0.7958 (p) cc_final: 0.7690 (t) REVERT: E 159 GLU cc_start: 0.7463 (pp20) cc_final: 0.7201 (pp20) REVERT: C 13 ARG cc_start: 0.7312 (ptp90) cc_final: 0.6548 (mpt180) REVERT: C 19 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7174 (pp30) REVERT: C 155 ASP cc_start: 0.8311 (m-30) cc_final: 0.7549 (m-30) REVERT: C 159 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: C 168 ARG cc_start: 0.8638 (tmt90) cc_final: 0.8388 (tmt90) REVERT: C 303 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.7748 (t0) REVERT: D 13 ARG cc_start: 0.7231 (ptp90) cc_final: 0.6657 (mtm-85) REVERT: D 44 MET cc_start: 0.8987 (mmt) cc_final: 0.8550 (mmm) REVERT: D 175 ASN cc_start: 0.8459 (m110) cc_final: 0.8119 (t0) REVERT: D 333 GLU cc_start: 0.7244 (tt0) cc_final: 0.6044 (pm20) outliers start: 18 outliers final: 7 residues processed: 217 average time/residue: 0.7494 time to fit residues: 176.7820 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 : 0.561 ------------------------------------------------------------------------------- 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: 0.9980 chunk 95 optimal weight: 5.9990 chunk 151 optimal weight: 0.0870 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106583 restraints weight = 34288.013| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.55 r_work: 0.3180 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1263 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= 0.173 Angle : 0.547 5.086 21375 Z= 0.305 Chirality : 0.039 0.166 2245 Planarity : 0.004 0.035 2530 Dihedral : 16.393 111.127 3271 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.18 % Allowed : 10.43 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.78 (0.20), residues: 1715 helix: 1.71 (0.14), residues: 1245 sheet: None (None), residues: 0 loop : -0.17 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 13 TYR 0.024 0.002 TYR A 97 PHE 0.020 0.002 PHE C 248 TRP 0.014 0.002 TRP C 94 HIS 0.005 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00345 (15945) covalent geometry : angle 0.54733 (21375) hydrogen bonds : bond 0.07281 ( 980) hydrogen bonds : angle 4.65177 ( 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 218 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7163 (ptp90) cc_final: 0.6450 (mtt90) REVERT: A 175 ASN cc_start: 0.8375 (m110) cc_final: 0.8094 (t0) REVERT: E 13 ARG cc_start: 0.7163 (ptp90) cc_final: 0.6488 (mtt90) REVERT: E 19 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.6746 (pm20) REVERT: E 78 VAL cc_start: 0.8002 (OUTLIER) cc_final: 0.7760 (t) REVERT: E 159 GLU cc_start: 0.7495 (pp20) cc_final: 0.7255 (pp20) REVERT: C 13 ARG cc_start: 0.7249 (ptp90) cc_final: 0.6497 (mpt180) REVERT: C 19 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7151 (pp30) REVERT: C 168 ARG cc_start: 0.8558 (tmt90) cc_final: 0.8320 (tmt90) REVERT: C 303 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7627 (t0) REVERT: C 325 MET cc_start: 0.9106 (mtp) cc_final: 0.8803 (mtp) REVERT: D 13 ARG cc_start: 0.7221 (ptp90) cc_final: 0.6645 (mtm-85) REVERT: D 19 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7111 (pm20) REVERT: D 44 MET cc_start: 0.9001 (mmt) cc_final: 0.8664 (mmm) REVERT: D 165 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7863 (mtt-85) REVERT: D 175 ASN cc_start: 0.8539 (m110) cc_final: 0.8164 (t0) REVERT: D 197 ARG cc_start: 0.8414 (ttm170) cc_final: 0.8072 (tpm170) REVERT: D 333 GLU cc_start: 0.7249 (tt0) cc_final: 0.5989 (pm20) outliers start: 18 outliers final: 9 residues processed: 208 average time/residue: 0.7609 time to fit residues: 171.9611 Evaluate side-chains 196 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 165 ARG 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: 0.6980 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3697 r_free = 0.3697 target = 0.137449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.107471 restraints weight = 31871.899| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.49 r_work: 0.3195 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 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 = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1342 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= 0.162 Angle : 0.526 5.576 21375 Z= 0.295 Chirality : 0.038 0.165 2245 Planarity : 0.004 0.037 2530 Dihedral : 15.609 107.082 3271 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.05 % Allowed : 10.43 % Favored : 88.52 % 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: 1.79 (0.20), residues: 1715 helix: 1.69 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : -0.06 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 13 TYR 0.023 0.002 TYR A 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 covalent geometry : bond 0.00320 (15945) covalent geometry : angle 0.52577 (21375) hydrogen bonds : bond 0.07042 ( 980) hydrogen bonds : angle 4.60858 ( 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 209 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7125 (ptp90) cc_final: 0.6411 (mtt180) REVERT: A 175 ASN cc_start: 0.8359 (m110) cc_final: 0.8082 (t0) REVERT: B 19 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: B 168 ARG cc_start: 0.8571 (tmt90) cc_final: 0.8260 (tmt90) REVERT: B 172 GLU cc_start: 0.8218 (mm-30) cc_final: 0.6826 (mp0) REVERT: E 13 ARG cc_start: 0.7171 (ptp90) cc_final: 0.6533 (mtt90) REVERT: E 19 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.6725 (pm20) REVERT: E 78 VAL cc_start: 0.7964 (OUTLIER) cc_final: 0.7723 (t) REVERT: E 159 GLU cc_start: 0.7459 (pp20) cc_final: 0.7159 (pp20) REVERT: E 172 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7828 (mm-30) REVERT: E 253 ILE cc_start: 0.8062 (mm) cc_final: 0.7825 (mm) REVERT: C 13 ARG cc_start: 0.7249 (ptp90) cc_final: 0.6516 (mpt180) REVERT: C 19 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7119 (pp30) REVERT: C 303 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7614 (t0) REVERT: C 325 MET cc_start: 0.9106 (mtp) cc_final: 0.8786 (mtp) REVERT: D 13 ARG cc_start: 0.7211 (ptp90) cc_final: 0.6645 (mtm-85) REVERT: D 44 MET cc_start: 0.9011 (mmt) cc_final: 0.8776 (mmt) REVERT: D 165 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7870 (mtt-85) REVERT: D 175 ASN cc_start: 0.8534 (m110) cc_final: 0.8167 (t0) REVERT: D 197 ARG cc_start: 0.8370 (ttm170) cc_final: 0.8006 (tpm170) REVERT: D 333 GLU cc_start: 0.7305 (tt0) cc_final: 0.6091 (pm20) outliers start: 16 outliers final: 8 residues processed: 198 average time/residue: 0.7425 time to fit residues: 159.6969 Evaluate side-chains 201 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 B residue 303 ASP 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 165 ARG 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: 0.6980 chunk 84 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3710 r_free = 0.3710 target = 0.138548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108247 restraints weight = 34210.475| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.54 r_work: 0.3205 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- 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 = 0.00 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 = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15945 Z= 0.148 Angle : 0.501 5.711 21375 Z= 0.282 Chirality : 0.037 0.164 2245 Planarity : 0.004 0.038 2530 Dihedral : 14.716 102.145 3271 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.92 % Allowed : 10.56 % Favored : 88.52 % 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: 1.87 (0.20), residues: 1715 helix: 1.74 (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 A 13 TYR 0.022 0.002 TYR C 97 PHE 0.017 0.002 PHE C 248 TRP 0.012 0.002 TRP B 94 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00287 (15945) covalent geometry : angle 0.50066 (21375) hydrogen bonds : bond 0.06720 ( 980) hydrogen bonds : angle 4.55093 ( 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 210 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7112 (ptp90) cc_final: 0.6380 (mtt90) REVERT: A 175 ASN cc_start: 0.8310 (m110) cc_final: 0.8040 (t0) REVERT: B 172 GLU cc_start: 0.8225 (mm-30) cc_final: 0.6832 (mp0) REVERT: E 13 ARG cc_start: 0.7164 (ptp90) cc_final: 0.6510 (mpt180) REVERT: E 19 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.6686 (pm20) REVERT: E 78 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7701 (t) REVERT: E 159 GLU cc_start: 0.7429 (pp20) cc_final: 0.7148 (pp20) REVERT: E 172 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7820 (mm-30) REVERT: E 253 ILE cc_start: 0.7990 (mm) cc_final: 0.7785 (mm) REVERT: C 13 ARG cc_start: 0.7222 (ptp90) cc_final: 0.6481 (mpt180) REVERT: C 168 ARG cc_start: 0.8602 (tmt90) cc_final: 0.8355 (tmt90) REVERT: C 303 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.7643 (t0) REVERT: C 325 MET cc_start: 0.9116 (mtp) cc_final: 0.8825 (mtp) REVERT: D 13 ARG cc_start: 0.7200 (ptp90) cc_final: 0.6557 (mtt90) REVERT: D 44 MET cc_start: 0.8979 (mmt) cc_final: 0.8722 (mmm) REVERT: D 165 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7820 (mtt-85) REVERT: D 175 ASN cc_start: 0.8516 (m110) cc_final: 0.8148 (t0) REVERT: D 197 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7991 (tpm170) REVERT: D 333 GLU cc_start: 0.7348 (tt0) cc_final: 0.6132 (pm20) outliers start: 14 outliers final: 8 residues processed: 200 average time/residue: 0.7400 time to fit residues: 160.9611 Evaluate side-chains 200 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 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 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 165 ARG Chi-restraints excluded: chain D residue 197 ARG 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: 2.9990 chunk 86 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 113 optimal weight: 0.0870 chunk 60 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3731 r_free = 0.3731 target = 0.140261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110931 restraints weight = 29656.894| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.43 r_work: 0.3246 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15945 Z= 0.130 Angle : 0.474 6.335 21375 Z= 0.269 Chirality : 0.036 0.163 2245 Planarity : 0.003 0.040 2530 Dihedral : 14.198 98.853 3271 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.18 % Allowed : 10.49 % Favored : 88.33 % 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: 1.93 (0.20), residues: 1715 helix: 1.80 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : -0.06 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 13 TYR 0.025 0.002 TYR B 236 PHE 0.015 0.002 PHE A 248 TRP 0.013 0.001 TRP B 94 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00242 (15945) covalent geometry : angle 0.47425 (21375) hydrogen bonds : bond 0.06278 ( 980) hydrogen bonds : angle 4.47882 ( 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 214 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ASN cc_start: 0.8288 (m110) cc_final: 0.8011 (t0) REVERT: A 324 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: B 19 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7455 (pm20) REVERT: B 223 MET cc_start: 0.9085 (mmm) cc_final: 0.8883 (mmm) REVERT: E 13 ARG cc_start: 0.7141 (ptp90) cc_final: 0.6494 (mpt180) REVERT: E 19 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.6738 (pm20) REVERT: E 78 VAL cc_start: 0.7864 (OUTLIER) cc_final: 0.7606 (t) REVERT: E 159 GLU cc_start: 0.7395 (pp20) cc_final: 0.7128 (pp20) REVERT: E 172 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7812 (mm-30) REVERT: C 13 ARG cc_start: 0.7174 (ptp90) cc_final: 0.6433 (mpt180) REVERT: C 19 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7574 (pm20) REVERT: C 165 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7571 (mtm-85) REVERT: C 168 ARG cc_start: 0.8602 (tmt90) cc_final: 0.8398 (tmt90) REVERT: C 303 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7442 (t0) REVERT: D 13 ARG cc_start: 0.7159 (ptp90) cc_final: 0.6608 (mtm-85) REVERT: D 19 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.6779 (pm20) REVERT: D 44 MET cc_start: 0.8948 (mmt) cc_final: 0.8637 (mmm) REVERT: D 165 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7751 (mtt-85) REVERT: D 175 ASN cc_start: 0.8471 (m110) cc_final: 0.8113 (t0) REVERT: D 197 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7953 (tpm170) REVERT: D 293 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8085 (tm130) REVERT: D 333 GLU cc_start: 0.7341 (tt0) cc_final: 0.6154 (pm20) outliers start: 18 outliers final: 6 residues processed: 202 average time/residue: 0.7112 time to fit residues: 156.8461 Evaluate side-chains 202 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS 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 C residue 19 GLN Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 165 ARG Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 165 ARG 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: 5.9990 chunk 139 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3708 r_free = 0.3708 target = 0.138434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108957 restraints weight = 29060.008| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.42 r_work: 0.3217 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1515 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= 0.152 Angle : 0.508 7.301 21375 Z= 0.286 Chirality : 0.038 0.164 2245 Planarity : 0.004 0.040 2530 Dihedral : 14.024 95.096 3271 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.18 % Allowed : 10.43 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.88 (0.20), residues: 1715 helix: 1.74 (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 0.000 ARG B 13 TYR 0.025 0.002 TYR B 236 PHE 0.017 0.002 PHE C 248 TRP 0.012 0.002 TRP C 94 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00296 (15945) covalent geometry : angle 0.50829 (21375) hydrogen bonds : bond 0.06802 ( 980) hydrogen bonds : angle 4.55712 ( 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 207 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7089 (ptp90) cc_final: 0.6391 (mtt90) REVERT: A 175 ASN cc_start: 0.8311 (m110) cc_final: 0.8040 (t0) REVERT: A 324 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: E 13 ARG cc_start: 0.7136 (ptp90) cc_final: 0.6493 (mpt180) REVERT: E 19 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.6693 (pm20) REVERT: E 159 GLU cc_start: 0.7400 (pp20) cc_final: 0.7134 (pp20) REVERT: E 172 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7785 (mm-30) REVERT: C 13 ARG cc_start: 0.7231 (ptp90) cc_final: 0.6530 (mpt180) REVERT: C 19 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7082 (pp30) REVERT: C 303 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7436 (t0) REVERT: C 325 MET cc_start: 0.9042 (mtp) cc_final: 0.8839 (mtp) REVERT: D 13 ARG cc_start: 0.7173 (ptp90) cc_final: 0.6604 (mtm-85) REVERT: D 44 MET cc_start: 0.8976 (mmt) cc_final: 0.8732 (mmm) REVERT: D 165 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7784 (mtt-85) REVERT: D 175 ASN cc_start: 0.8496 (m110) cc_final: 0.8135 (t0) REVERT: D 197 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7953 (tpm170) REVERT: D 293 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8127 (tm130) REVERT: D 333 GLU cc_start: 0.7365 (tt0) cc_final: 0.6113 (pm20) outliers start: 18 outliers final: 7 residues processed: 196 average time/residue: 0.7633 time to fit residues: 162.4208 Evaluate side-chains 201 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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 165 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 76 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 140 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3784 r_free = 0.3784 target = 0.142594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114193 restraints weight = 34179.230| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.47 r_work: 0.3300 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15945 Z= 0.133 Angle : 0.483 7.095 21375 Z= 0.273 Chirality : 0.037 0.163 2245 Planarity : 0.003 0.041 2530 Dihedral : 13.706 93.299 3271 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.85 % Allowed : 10.69 % 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: 1.91 (0.20), residues: 1715 helix: 1.78 (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 0.004 0.000 ARG B 13 TYR 0.028 0.002 TYR B 236 PHE 0.015 0.002 PHE A 248 TRP 0.012 0.002 TRP B 94 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00250 (15945) covalent geometry : angle 0.48298 (21375) hydrogen bonds : bond 0.06375 ( 980) hydrogen bonds : angle 4.49269 ( 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 201 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7150 (ptp90) cc_final: 0.6490 (mtt90) REVERT: A 175 ASN cc_start: 0.8295 (m110) cc_final: 0.8072 (t0) REVERT: A 324 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: B 19 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: B 223 MET cc_start: 0.9092 (mmm) cc_final: 0.8883 (mmm) REVERT: E 13 ARG cc_start: 0.7219 (ptp90) cc_final: 0.6575 (mpt180) REVERT: E 19 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.6705 (pm20) REVERT: E 159 GLU cc_start: 0.7493 (pp20) cc_final: 0.7257 (pp20) REVERT: C 13 ARG cc_start: 0.7315 (ptp90) cc_final: 0.6623 (mpt180) REVERT: C 19 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7123 (pp30) REVERT: C 303 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7525 (t0) REVERT: D 13 ARG cc_start: 0.7217 (ptp90) cc_final: 0.6649 (mtm-85) REVERT: D 44 MET cc_start: 0.8968 (mmt) cc_final: 0.8670 (mmm) REVERT: D 165 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7805 (mtt-85) REVERT: D 175 ASN cc_start: 0.8493 (m110) cc_final: 0.8189 (t0) REVERT: D 197 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7977 (tpm170) REVERT: D 293 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8123 (tm130) REVERT: D 333 GLU cc_start: 0.7459 (tt0) cc_final: 0.6274 (pm20) outliers start: 13 outliers final: 4 residues processed: 192 average time/residue: 0.7356 time to fit residues: 154.1842 Evaluate side-chains 194 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 165 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 43 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3780 r_free = 0.3780 target = 0.142314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.113579 restraints weight = 40502.273| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.58 r_work: 0.3285 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1612 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= 0.136 Angle : 0.487 7.528 21375 Z= 0.275 Chirality : 0.037 0.162 2245 Planarity : 0.003 0.040 2530 Dihedral : 13.334 90.741 3267 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.92 % Allowed : 10.69 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.92 (0.20), residues: 1715 helix: 1.79 (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 13 TYR 0.031 0.002 TYR B 236 PHE 0.015 0.002 PHE A 248 TRP 0.012 0.002 TRP C 94 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00257 (15945) covalent geometry : angle 0.48736 (21375) hydrogen bonds : bond 0.06425 ( 980) hydrogen bonds : angle 4.49322 ( 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 209 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7184 (ptp90) cc_final: 0.6494 (mtt90) REVERT: A 175 ASN cc_start: 0.8310 (m110) cc_final: 0.8076 (t0) REVERT: A 324 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: B 172 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7880 (mm-30) REVERT: E 13 ARG cc_start: 0.7202 (ptp90) cc_final: 0.6573 (mpt180) REVERT: E 19 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.6714 (pm20) REVERT: E 159 GLU cc_start: 0.7518 (pp20) cc_final: 0.7276 (pp20) REVERT: E 172 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7822 (mm-30) REVERT: C 13 ARG cc_start: 0.7339 (ptp90) cc_final: 0.6648 (mpt180) REVERT: C 19 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: C 303 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7529 (t0) REVERT: D 13 ARG cc_start: 0.7288 (ptp90) cc_final: 0.6689 (mtm-85) REVERT: D 44 MET cc_start: 0.8966 (mmt) cc_final: 0.8668 (mmm) REVERT: D 165 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7846 (mtt-85) REVERT: D 175 ASN cc_start: 0.8527 (m110) cc_final: 0.8184 (t0) REVERT: D 197 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7988 (tpm170) REVERT: D 293 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8135 (tm130) REVERT: D 333 GLU cc_start: 0.7459 (tt0) cc_final: 0.6239 (pm20) outliers start: 14 outliers final: 6 residues processed: 199 average time/residue: 0.7210 time to fit residues: 156.5904 Evaluate side-chains 204 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 165 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 chunk 135 optimal weight: 0.0030 chunk 165 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 175 ASN E 71 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 = 0.3726 r_free = 0.3726 target = 0.139838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109320 restraints weight = 36426.086| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.59 r_work: 0.3220 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.402 15945 Z= 0.246 Angle : 0.719 65.899 21375 Z= 0.427 Chirality : 0.037 0.207 2245 Planarity : 0.006 0.240 2530 Dihedral : 13.334 90.735 3267 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.05 % Allowed : 10.75 % Favored : 88.20 % Cbeta Deviations : 0.06 % 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: 1.92 (0.19), residues: 1715 helix: 1.79 (0.14), residues: 1250 sheet: None (None), residues: 0 loop : -0.05 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 13 TYR 0.030 0.002 TYR B 236 PHE 0.015 0.002 PHE A 248 TRP 0.012 0.002 TRP C 94 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00502 (15945) covalent geometry : angle 0.71884 (21375) hydrogen bonds : bond 0.06429 ( 980) hydrogen bonds : angle 4.49342 ( 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 208 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7116 (ptp90) cc_final: 0.6402 (mtt90) REVERT: A 175 ASN cc_start: 0.8280 (m110) cc_final: 0.8022 (t0) REVERT: A 324 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: B 172 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7851 (mm-30) REVERT: E 13 ARG cc_start: 0.7149 (ptp90) cc_final: 0.6521 (mpt180) REVERT: E 19 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.6694 (pm20) REVERT: E 159 GLU cc_start: 0.7451 (pp20) cc_final: 0.7185 (pp20) REVERT: E 172 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7788 (mm-30) REVERT: C 13 ARG cc_start: 0.7262 (ptp90) cc_final: 0.6539 (mpt180) REVERT: C 19 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7615 (pm20) REVERT: C 303 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7453 (t0) REVERT: D 13 ARG cc_start: 0.7261 (ptp90) cc_final: 0.6642 (mtm-85) REVERT: D 44 MET cc_start: 0.8956 (mmt) cc_final: 0.8656 (mmm) REVERT: D 165 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7797 (mtt-85) REVERT: D 175 ASN cc_start: 0.8511 (m110) cc_final: 0.8141 (t0) REVERT: D 197 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7957 (tpm170) REVERT: D 293 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8098 (tm130) REVERT: D 333 GLU cc_start: 0.7395 (tt0) cc_final: 0.6170 (pm20) outliers start: 16 outliers final: 5 residues processed: 196 average time/residue: 0.7326 time to fit residues: 156.4965 Evaluate side-chains 203 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 87 THR Chi-restraints excluded: chain D residue 165 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 30 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN B 173 ASN B 175 ASN E 71 GLN E 173 ASN E 175 ASN C 175 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.140405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.112560 restraints weight = 27326.961| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.31 r_work: 0.3290 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15945 Z= 0.161 Angle : 0.531 7.976 21375 Z= 0.296 Chirality : 0.038 0.164 2245 Planarity : 0.004 0.041 2530 Dihedral : 13.432 90.429 3267 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.05 % Allowed : 10.69 % Favored : 88.26 % 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: 1.82 (0.19), residues: 1715 helix: 1.76 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -0.11 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 13 TYR 0.032 0.002 TYR B 236 PHE 0.020 0.002 PHE E 42 TRP 0.016 0.002 TRP E 287 HIS 0.004 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00320 (15945) covalent geometry : angle 0.53080 (21375) hydrogen bonds : bond 0.06974 ( 980) hydrogen bonds : angle 4.57742 ( 2830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7211.17 seconds wall clock time: 123 minutes 8.89 seconds (7388.89 seconds total)