Starting phenix.real_space_refine on Mon Jul 6 00:46:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lj1_63130/07_2026/9lj1_63130_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lj1_63130/07_2026/9lj1_63130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lj1_63130/07_2026/9lj1_63130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lj1_63130/07_2026/9lj1_63130.map" model { file = "/net/cci-nas-00/data/ceres_data/9lj1_63130/07_2026/9lj1_63130_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lj1_63130/07_2026/9lj1_63130_trim.cif" } resolution = 3.2 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= 0.000 sd= 0.002 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 P 12 5.49 5 S 88 5.16 5 C 10236 2.51 5 N 2692 2.21 5 O 2852 1.98 5 F 4 1.80 5 H 15688 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31572 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5691 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 9, 'TRANS': 334} Chain breaks: 1 Chain: "E" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 5691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5691 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 9, 'TRANS': 334} Chain breaks: 1 Chain: "C" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 5691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5691 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 9, 'TRANS': 334} Chain breaks: 1 Chain: "F" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 5691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5691 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 9, 'TRANS': 334} Chain breaks: 1 Chain: "H" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2130 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'9MF': 2, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'9MF': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'9MF': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.59, per 1000 atoms: 0.15 Number of scatterers: 31572 At special positions: 0 Unit cell: (123.69, 123.69, 124.62, 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) S 88 16.00 P 12 15.00 F 4 9.00 O 2852 8.00 N 2692 7.00 C 10236 6.00 H 15688 1.00 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: 2.44 Conformation dependent library (CDL) restraints added in 723.8 milliseconds 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 83.9% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 103 through 121 Processing helix chain 'A' and resid 124 through 149 removed outlier: 3.602A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 185 removed outlier: 3.707A pdb=" N ILE A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 199 Processing helix chain 'A' and resid 200 through 223 Processing helix chain 'A' and resid 224 through 237 removed outlier: 4.267A pdb=" N ARG A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 249 through 262 Processing helix chain 'A' and resid 262 through 289 Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 321 through 363 Proline residue: A 342 - end of helix Processing helix chain 'A' and resid 366 through 384 Processing helix chain 'A' and resid 516 through 542 removed outlier: 3.651A pdb=" N LEU A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 576 removed outlier: 3.687A pdb=" N VAL A 549 " --> pdb=" O ASP A 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 22 Processing helix chain 'E' and resid 29 through 39 Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.512A pdb=" N VAL E 56 " --> pdb=" O MET E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 removed outlier: 3.658A pdb=" N ARG E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 93 removed outlier: 4.031A pdb=" N PHE E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 113 Processing helix chain 'E' and resid 118 through 129 removed outlier: 3.794A pdb=" N ALA E 129 " --> pdb=" O MET E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 147 Processing helix chain 'B' and resid 104 through 121 Processing helix chain 'B' and resid 124 through 149 removed outlier: 3.602A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 149 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 185 removed outlier: 3.707A pdb=" N ILE B 162 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 199 Processing helix chain 'B' and resid 200 through 223 Processing helix chain 'B' and resid 224 through 237 removed outlier: 4.267A pdb=" N ARG B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 237 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 249 through 262 Processing helix chain 'B' and resid 262 through 289 Processing helix chain 'B' and resid 297 through 310 Processing helix chain 'B' and resid 321 through 363 Proline residue: B 342 - end of helix Processing helix chain 'B' and resid 366 through 384 Processing helix chain 'B' and resid 516 through 542 removed outlier: 3.651A pdb=" N LEU B 541 " --> pdb=" O PHE B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 576 removed outlier: 3.687A pdb=" N VAL B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 22 Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 45 through 57 removed outlier: 3.512A pdb=" N VAL C 56 " --> pdb=" O MET C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 75 removed outlier: 3.658A pdb=" N ARG C 75 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 93 removed outlier: 4.031A pdb=" N PHE C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 113 Processing helix chain 'C' and resid 118 through 129 removed outlier: 3.794A pdb=" N ALA C 129 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 147 Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 124 through 149 removed outlier: 3.602A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE D 149 " --> pdb=" O VAL D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 185 removed outlier: 3.707A pdb=" N ILE D 162 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 199 Processing helix chain 'D' and resid 200 through 223 Processing helix chain 'D' and resid 224 through 237 removed outlier: 4.267A pdb=" N ARG D 232 " --> pdb=" O THR D 228 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 246 Processing helix chain 'D' and resid 249 through 262 Processing helix chain 'D' and resid 262 through 289 Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 321 through 363 Proline residue: D 342 - end of helix Processing helix chain 'D' and resid 366 through 384 Processing helix chain 'D' and resid 516 through 542 removed outlier: 3.651A pdb=" N LEU D 541 " --> pdb=" O PHE D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 576 removed outlier: 3.687A pdb=" N VAL D 549 " --> pdb=" O ASP D 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 22 Processing helix chain 'F' and resid 29 through 39 Processing helix chain 'F' and resid 45 through 57 removed outlier: 3.512A pdb=" N VAL F 56 " --> pdb=" O MET F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 75 removed outlier: 3.658A pdb=" N ARG F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 removed outlier: 4.031A pdb=" N PHE F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 118 through 129 removed outlier: 3.794A pdb=" N ALA F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'G' and resid 104 through 121 Processing helix chain 'G' and resid 124 through 149 removed outlier: 3.602A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE G 149 " --> pdb=" O VAL G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 185 removed outlier: 3.707A pdb=" N ILE G 162 " --> pdb=" O SER G 158 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS G 185 " --> pdb=" O SER G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 199 Processing helix chain 'G' and resid 200 through 223 Processing helix chain 'G' and resid 224 through 237 removed outlier: 4.267A pdb=" N ARG G 232 " --> pdb=" O THR G 228 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER G 233 " --> pdb=" O SER G 229 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU G 237 " --> pdb=" O SER G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 246 Processing helix chain 'G' and resid 249 through 262 Processing helix chain 'G' and resid 262 through 289 Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 321 through 363 Proline residue: G 342 - end of helix Processing helix chain 'G' and resid 366 through 384 Processing helix chain 'G' and resid 516 through 542 removed outlier: 3.651A pdb=" N LEU G 541 " --> pdb=" O PHE G 537 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 576 removed outlier: 3.687A pdb=" N VAL G 549 " --> pdb=" O ASP G 545 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 22 Processing helix chain 'H' and resid 29 through 39 Processing helix chain 'H' and resid 45 through 57 removed outlier: 3.512A pdb=" N VAL H 56 " --> pdb=" O MET H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 75 removed outlier: 3.658A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 removed outlier: 4.031A pdb=" N PHE H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 113 Processing helix chain 'H' and resid 118 through 129 removed outlier: 3.794A pdb=" N ALA H 129 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 147 Processing sheet with id=AA1, first strand: chain 'E' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'F' and resid 27 through 28 Processing sheet with id=AA6, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'H' and resid 27 through 28 Processing sheet with id=AA8, first strand: chain 'H' and resid 100 through 102 1233 hydrogen bonds defined for protein. 3687 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: 5.81 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 15656 1.02 - 1.22: 60 1.22 - 1.42: 6768 1.42 - 1.62: 9252 1.62 - 1.82: 160 Bond restraints: 31896 Sorted by residual: bond pdb=" SG CYS B 562 " pdb=" HG CYS B 562 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" SG CYS A 562 " pdb=" HG CYS A 562 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" SG CYS D 562 " pdb=" HG CYS D 562 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" SG CYS G 562 " pdb=" HG CYS G 562 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" ND2 ASN B 224 " pdb="HD21 ASN B 224 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 ... (remaining 31891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.05: 57204 4.05 - 8.10: 128 8.10 - 12.15: 56 12.15 - 16.20: 8 16.20 - 20.25: 4 Bond angle restraints: 57400 Sorted by residual: angle pdb=" O11 PIO G1000 " pdb=" P1 PIO G1000 " pdb=" O12 PIO G1000 " ideal model delta sigma weight residual 121.09 100.84 20.25 3.00e+00 1.11e-01 4.56e+01 angle pdb=" O11 PIO A 802 " pdb=" P1 PIO A 802 " pdb=" O12 PIO A 802 " ideal model delta sigma weight residual 121.09 100.84 20.25 3.00e+00 1.11e-01 4.56e+01 angle pdb=" O11 PIO D 801 " pdb=" P1 PIO D 801 " pdb=" O12 PIO D 801 " ideal model delta sigma weight residual 121.09 100.84 20.25 3.00e+00 1.11e-01 4.56e+01 angle pdb=" O11 PIO B 801 " pdb=" P1 PIO B 801 " pdb=" O12 PIO B 801 " ideal model delta sigma weight residual 121.09 100.84 20.25 3.00e+00 1.11e-01 4.56e+01 angle pdb=" C ILE A 574 " pdb=" CA ILE A 574 " pdb=" CB ILE A 574 " ideal model delta sigma weight residual 111.97 104.84 7.13 1.28e+00 6.10e-01 3.10e+01 ... (remaining 57395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 13008 15.95 - 31.90: 1164 31.90 - 47.85: 424 47.85 - 63.80: 196 63.80 - 79.75: 28 Dihedral angle restraints: 14820 sinusoidal: 8008 harmonic: 6812 Sorted by residual: dihedral pdb=" CA CYS B 184 " pdb=" C CYS B 184 " pdb=" N CYS B 185 " pdb=" CA CYS B 185 " ideal model delta harmonic sigma weight residual 180.00 -164.22 -15.78 0 5.00e+00 4.00e-02 9.96e+00 dihedral pdb=" CA CYS D 184 " pdb=" C CYS D 184 " pdb=" N CYS D 185 " pdb=" CA CYS D 185 " ideal model delta harmonic sigma weight residual 180.00 -164.22 -15.78 0 5.00e+00 4.00e-02 9.96e+00 dihedral pdb=" CA CYS A 184 " pdb=" C CYS A 184 " pdb=" N CYS A 185 " pdb=" CA CYS A 185 " ideal model delta harmonic sigma weight residual 180.00 -164.22 -15.78 0 5.00e+00 4.00e-02 9.96e+00 ... (remaining 14817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1652 0.033 - 0.066: 528 0.066 - 0.099: 188 0.099 - 0.132: 56 0.132 - 0.165: 20 Chirality restraints: 2444 Sorted by residual: chirality pdb=" CA PHE G 171 " pdb=" N PHE G 171 " pdb=" C PHE G 171 " pdb=" CB PHE G 171 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA PHE D 171 " pdb=" N PHE D 171 " pdb=" C PHE D 171 " pdb=" CB PHE D 171 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA PHE A 171 " pdb=" N PHE A 171 " pdb=" C PHE A 171 " pdb=" CB PHE A 171 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 ... (remaining 2441 not shown) Planarity restraints: 4624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 238 " -0.160 2.00e-02 2.50e+03 1.82e-01 4.96e+02 pdb=" CD GLN A 238 " 0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN A 238 " 0.158 2.00e-02 2.50e+03 pdb=" NE2 GLN A 238 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN A 238 " 0.270 2.00e-02 2.50e+03 pdb="HE22 GLN A 238 " -0.274 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 238 " 0.160 2.00e-02 2.50e+03 1.82e-01 4.96e+02 pdb=" CD GLN D 238 " -0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN D 238 " -0.158 2.00e-02 2.50e+03 pdb=" NE2 GLN D 238 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN D 238 " -0.270 2.00e-02 2.50e+03 pdb="HE22 GLN D 238 " 0.274 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 238 " -0.160 2.00e-02 2.50e+03 1.82e-01 4.96e+02 pdb=" CD GLN G 238 " 0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN G 238 " 0.158 2.00e-02 2.50e+03 pdb=" NE2 GLN G 238 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN G 238 " 0.270 2.00e-02 2.50e+03 pdb="HE22 GLN G 238 " -0.274 2.00e-02 2.50e+03 ... (remaining 4621 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 3739 2.23 - 2.82: 72270 2.82 - 3.42: 88829 3.42 - 4.01: 112866 4.01 - 4.60: 176043 Nonbonded interactions: 453747 Sorted by model distance: nonbonded pdb=" OD1 ASN F 138 " pdb=" H GLU F 140 " model vdw 1.639 2.450 nonbonded pdb=" OD1 ASN C 138 " pdb=" H GLU C 140 " model vdw 1.639 2.450 nonbonded pdb=" OD1 ASN H 138 " pdb=" H GLU H 140 " model vdw 1.639 2.450 nonbonded pdb=" OD1 ASN E 138 " pdb=" H GLU E 140 " model vdw 1.639 2.450 nonbonded pdb="HE22 GLN G 375 " pdb=" O LEU H 113 " model vdw 1.644 2.450 ... (remaining 453742 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 103 through 576) selection = (chain 'B' and resid 103 through 576) selection = (chain 'D' and resid 103 through 576) selection = (chain 'G' and resid 103 through 576) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 0.210 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.610 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 : 0.007 0.094 16208 Z= 0.378 Angle : 0.976 20.254 21888 Z= 0.481 Chirality : 0.040 0.165 2444 Planarity : 0.005 0.074 2728 Dihedral : 15.631 79.751 5908 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.98 % Allowed : 17.07 % Favored : 81.95 % 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: 1.32 (0.20), residues: 1928 helix: 1.20 (0.13), residues: 1580 sheet: None (None), residues: 0 loop : -0.33 (0.38), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 570 TYR 0.009 0.001 TYR B 271 PHE 0.019 0.001 PHE D 171 TRP 0.006 0.002 TRP A 180 HIS 0.004 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00710 / 0.38 (16208) covalent geometry : angle 0.97585 / 0.48 (21888) hydrogen bonds : bond 0.09837 / 6.70 ( 1233) hydrogen bonds : angle 6.05212 / 4.44 ( 3687) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 303 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 287 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 GLU cc_start: 0.7686 (tp30) cc_final: 0.6489 (mt-10) REVERT: B 551 GLU cc_start: 0.7675 (tp30) cc_final: 0.6476 (mt-10) REVERT: D 551 GLU cc_start: 0.7662 (tp30) cc_final: 0.6468 (mt-10) REVERT: G 551 GLU cc_start: 0.7675 (tp30) cc_final: 0.6494 (mt-10) outliers start: 16 outliers final: 12 residues processed: 303 average time/residue: 0.2380 time to fit residues: 111.1335 Evaluate side-chains 253 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 241 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 244 ARG Chi-restraints excluded: chain G residue 567 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN B 112 GLN D 112 GLN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.245189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144451 restraints weight = 63333.224| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.09 r_work: 0.3400 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16208 Z= 0.150 Angle : 0.509 6.054 21888 Z= 0.277 Chirality : 0.034 0.146 2444 Planarity : 0.004 0.051 2728 Dihedral : 7.668 59.153 2276 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.62 % Allowed : 17.20 % Favored : 80.18 % 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: 1.94 (0.19), residues: 1928 helix: 1.67 (0.13), residues: 1584 sheet: None (None), residues: 0 loop : -0.37 (0.39), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 241 TYR 0.013 0.001 TYR A 108 PHE 0.015 0.001 PHE G 171 TRP 0.011 0.001 TRP G 180 HIS 0.005 0.001 HIS G 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (16208) covalent geometry : angle 0.50922 / 0.28 (21888) hydrogen bonds : bond 0.04693 / 3.09 ( 1233) hydrogen bonds : angle 5.04037 / 3.74 ( 3687) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 324 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 GLU cc_start: 0.7747 (tp30) cc_final: 0.6566 (mt-10) REVERT: B 551 GLU cc_start: 0.7718 (tp30) cc_final: 0.6547 (mt-10) REVERT: D 551 GLU cc_start: 0.7668 (tp30) cc_final: 0.6484 (mt-10) REVERT: G 551 GLU cc_start: 0.7685 (tp30) cc_final: 0.6514 (mt-10) outliers start: 43 outliers final: 30 residues processed: 289 average time/residue: 0.2612 time to fit residues: 112.2624 Evaluate side-chains 270 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 244 ARG Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 45 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 11 optimal weight: 0.0070 chunk 178 optimal weight: 50.0000 chunk 166 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4883 r_free = 0.4883 target = 0.247762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.146934 restraints weight = 63089.813| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.30 r_work: 0.3436 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16208 Z= 0.129 Angle : 0.471 5.912 21888 Z= 0.257 Chirality : 0.033 0.145 2444 Planarity : 0.004 0.041 2728 Dihedral : 7.300 58.697 2260 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.66 % Allowed : 16.28 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.20), residues: 1928 helix: 1.97 (0.13), residues: 1592 sheet: None (None), residues: 0 loop : -0.23 (0.40), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 241 TYR 0.013 0.001 TYR A 108 PHE 0.011 0.001 PHE G 171 TRP 0.007 0.001 TRP D 180 HIS 0.003 0.001 HIS B 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (16208) covalent geometry : angle 0.47116 / 0.26 (21888) hydrogen bonds : bond 0.04380 / 2.89 ( 1233) hydrogen bonds : angle 4.86773 / 3.61 ( 3687) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 309 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 249 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 GLU cc_start: 0.7780 (tp30) cc_final: 0.6568 (mt-10) REVERT: B 551 GLU cc_start: 0.7767 (tp30) cc_final: 0.6559 (mt-10) REVERT: C 20 PHE cc_start: -0.5770 (OUTLIER) cc_final: -0.5983 (t80) REVERT: D 108 TYR cc_start: 0.6033 (OUTLIER) cc_final: 0.5542 (t80) REVERT: D 551 GLU cc_start: 0.7758 (tp30) cc_final: 0.6546 (mt-10) REVERT: F 20 PHE cc_start: -0.5801 (OUTLIER) cc_final: -0.6008 (t80) REVERT: F 94 ASP cc_start: 0.2476 (OUTLIER) cc_final: 0.2007 (t0) REVERT: G 108 TYR cc_start: 0.6041 (OUTLIER) cc_final: 0.5547 (t80) REVERT: G 551 GLU cc_start: 0.7774 (tp30) cc_final: 0.6580 (mt-10) REVERT: H 94 ASP cc_start: 0.2467 (OUTLIER) cc_final: 0.2004 (t0) outliers start: 60 outliers final: 40 residues processed: 279 average time/residue: 0.2599 time to fit residues: 108.9480 Evaluate side-chains 282 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 244 ARG Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 244 ARG Chi-restraints excluded: chain G residue 325 ARG Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 94 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 22 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 82 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.244755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.148481 restraints weight = 62607.208| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 4.31 r_work: 0.3315 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16208 Z= 0.226 Angle : 0.518 6.346 21888 Z= 0.285 Chirality : 0.035 0.140 2444 Planarity : 0.004 0.040 2728 Dihedral : 7.253 79.895 2260 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.78 % Allowed : 16.16 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.19), residues: 1928 helix: 1.95 (0.13), residues: 1584 sheet: None (None), residues: 0 loop : -0.43 (0.39), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 325 TYR 0.013 0.001 TYR A 108 PHE 0.013 0.001 PHE A 171 TRP 0.010 0.001 TRP G 322 HIS 0.003 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.23 (16208) covalent geometry : angle 0.51836 / 0.28 (21888) hydrogen bonds : bond 0.04702 / 3.08 ( 1233) hydrogen bonds : angle 4.92432 / 3.65 ( 3687) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 302 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 240 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8524 (t0) cc_final: 0.8298 (t0) REVERT: A 551 GLU cc_start: 0.7706 (tp30) cc_final: 0.6485 (mt-10) REVERT: B 551 GLU cc_start: 0.7687 (tp30) cc_final: 0.6472 (mt-10) REVERT: C 20 PHE cc_start: -0.5786 (OUTLIER) cc_final: -0.6009 (t80) REVERT: D 108 TYR cc_start: 0.6206 (OUTLIER) cc_final: 0.5493 (t80) REVERT: D 551 GLU cc_start: 0.7674 (tp30) cc_final: 0.6464 (mt-10) REVERT: F 20 PHE cc_start: -0.5776 (OUTLIER) cc_final: -0.6003 (t80) REVERT: F 94 ASP cc_start: 0.2582 (OUTLIER) cc_final: 0.2187 (t0) REVERT: G 108 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.5503 (t80) REVERT: G 551 GLU cc_start: 0.7696 (tp30) cc_final: 0.6492 (mt-10) REVERT: H 94 ASP cc_start: 0.2576 (OUTLIER) cc_final: 0.2182 (t0) outliers start: 62 outliers final: 34 residues processed: 267 average time/residue: 0.2608 time to fit residues: 104.4849 Evaluate side-chains 273 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 325 ARG Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 94 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 176 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 137 optimal weight: 30.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.245445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.153841 restraints weight = 62480.329| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 5.97 r_work: 0.3301 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16208 Z= 0.192 Angle : 0.485 5.838 21888 Z= 0.268 Chirality : 0.034 0.141 2444 Planarity : 0.004 0.041 2728 Dihedral : 6.130 54.657 2244 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.60 % Allowed : 17.13 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.19), residues: 1928 helix: 2.02 (0.13), residues: 1584 sheet: None (None), residues: 0 loop : -0.41 (0.39), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 325 TYR 0.012 0.001 TYR A 108 PHE 0.015 0.001 PHE A 171 TRP 0.007 0.001 TRP A 322 HIS 0.002 0.001 HIS G 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (16208) covalent geometry : angle 0.48506 / 0.27 (21888) hydrogen bonds : bond 0.04515 / 2.97 ( 1233) hydrogen bonds : angle 4.83928 / 3.59 ( 3687) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 294 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 235 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 GLU cc_start: 0.7773 (tp30) cc_final: 0.6533 (mt-10) REVERT: B 108 TYR cc_start: 0.6129 (OUTLIER) cc_final: 0.5579 (t80) REVERT: B 551 GLU cc_start: 0.7756 (tp30) cc_final: 0.6524 (mt-10) REVERT: C 20 PHE cc_start: -0.5799 (OUTLIER) cc_final: -0.6013 (t80) REVERT: D 551 GLU cc_start: 0.7740 (tp30) cc_final: 0.6516 (mt-10) REVERT: F 94 ASP cc_start: 0.2489 (OUTLIER) cc_final: 0.2109 (t0) REVERT: G 551 GLU cc_start: 0.7762 (tp30) cc_final: 0.6538 (mt-10) REVERT: H 94 ASP cc_start: 0.2497 (OUTLIER) cc_final: 0.2123 (t0) outliers start: 59 outliers final: 50 residues processed: 268 average time/residue: 0.2404 time to fit residues: 98.0755 Evaluate side-chains 283 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 325 ARG Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 94 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 166 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.246332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.148028 restraints weight = 62355.192| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.20 r_work: 0.3351 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16208 Z= 0.169 Angle : 0.473 4.614 21888 Z= 0.261 Chirality : 0.034 0.143 2444 Planarity : 0.003 0.039 2728 Dihedral : 5.898 52.059 2244 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.72 % Allowed : 17.44 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.19), residues: 1928 helix: 2.10 (0.13), residues: 1588 sheet: None (None), residues: 0 loop : -0.32 (0.39), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 235 TYR 0.008 0.001 TYR A 108 PHE 0.016 0.001 PHE B 171 TRP 0.007 0.001 TRP G 322 HIS 0.002 0.001 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (16208) covalent geometry : angle 0.47304 / 0.26 (21888) hydrogen bonds : bond 0.04396 / 2.89 ( 1233) hydrogen bonds : angle 4.75290 / 3.53 ( 3687) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 301 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 240 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.5996 (OUTLIER) cc_final: 0.5445 (t80) REVERT: A 551 GLU cc_start: 0.7817 (tp30) cc_final: 0.6559 (mt-10) REVERT: B 108 TYR cc_start: 0.6145 (OUTLIER) cc_final: 0.5500 (t80) REVERT: B 551 GLU cc_start: 0.7809 (tp30) cc_final: 0.6565 (mt-10) REVERT: D 551 GLU cc_start: 0.7819 (tp30) cc_final: 0.6597 (mt-10) REVERT: F 20 PHE cc_start: -0.5828 (OUTLIER) cc_final: -0.6065 (t80) REVERT: F 94 ASP cc_start: 0.2437 (OUTLIER) cc_final: 0.2054 (t0) REVERT: G 551 GLU cc_start: 0.7799 (tp30) cc_final: 0.6566 (mt-10) REVERT: H 94 ASP cc_start: 0.2536 (OUTLIER) cc_final: 0.2167 (t0) outliers start: 61 outliers final: 47 residues processed: 270 average time/residue: 0.2310 time to fit residues: 95.0822 Evaluate side-chains 284 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 232 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 325 ARG Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 94 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 36 optimal weight: 7.9990 chunk 157 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 91 optimal weight: 40.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.246924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.146760 restraints weight = 62638.432| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.70 r_work: 0.3378 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16208 Z= 0.150 Angle : 0.467 4.628 21888 Z= 0.258 Chirality : 0.033 0.143 2444 Planarity : 0.003 0.039 2728 Dihedral : 5.722 48.438 2244 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.54 % Allowed : 17.62 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.19), residues: 1928 helix: 2.14 (0.13), residues: 1588 sheet: None (None), residues: 0 loop : -0.31 (0.39), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 325 TYR 0.006 0.001 TYR G 129 PHE 0.013 0.001 PHE B 171 TRP 0.006 0.001 TRP G 322 HIS 0.002 0.001 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (16208) covalent geometry : angle 0.46728 / 0.26 (21888) hydrogen bonds : bond 0.04320 / 2.84 ( 1233) hydrogen bonds : angle 4.69680 / 3.49 ( 3687) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 239 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.6090 (OUTLIER) cc_final: 0.5569 (t80) REVERT: A 551 GLU cc_start: 0.7846 (tp30) cc_final: 0.6636 (mt-10) REVERT: B 108 TYR cc_start: 0.6114 (OUTLIER) cc_final: 0.5493 (t80) REVERT: B 551 GLU cc_start: 0.7831 (tp30) cc_final: 0.6624 (mt-10) REVERT: C 20 PHE cc_start: -0.5916 (OUTLIER) cc_final: -0.6141 (t80) REVERT: D 551 GLU cc_start: 0.7819 (tp30) cc_final: 0.6619 (mt-10) REVERT: F 20 PHE cc_start: -0.5938 (OUTLIER) cc_final: -0.6160 (t80) REVERT: F 94 ASP cc_start: 0.2553 (OUTLIER) cc_final: 0.2182 (t0) REVERT: G 551 GLU cc_start: 0.7833 (tp30) cc_final: 0.6637 (mt-10) REVERT: H 94 ASP cc_start: 0.2612 (OUTLIER) cc_final: 0.2230 (t0) outliers start: 58 outliers final: 44 residues processed: 265 average time/residue: 0.2449 time to fit residues: 99.8187 Evaluate side-chains 279 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 325 ARG Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 94 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 187 optimal weight: 40.0000 chunk 189 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 86 optimal weight: 30.0000 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.243824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.141250 restraints weight = 62554.785| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.25 r_work: 0.3353 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16208 Z= 0.284 Angle : 0.549 6.652 21888 Z= 0.304 Chirality : 0.037 0.158 2444 Planarity : 0.004 0.037 2728 Dihedral : 6.001 52.796 2244 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.48 % Allowed : 17.74 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.19), residues: 1928 helix: 1.97 (0.13), residues: 1584 sheet: None (None), residues: 0 loop : -0.80 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 325 TYR 0.011 0.001 TYR G 129 PHE 0.014 0.001 PHE B 171 TRP 0.011 0.002 TRP G 322 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.28 (16208) covalent geometry : angle 0.54897 / 0.30 (21888) hydrogen bonds : bond 0.04800 / 3.14 ( 1233) hydrogen bonds : angle 4.88958 / 3.64 ( 3687) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 228 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 TYR cc_start: 0.6213 (OUTLIER) cc_final: 0.5519 (t80) REVERT: A 551 GLU cc_start: 0.7815 (tp30) cc_final: 0.6539 (mt-10) REVERT: B 551 GLU cc_start: 0.7795 (tp30) cc_final: 0.6530 (mt-10) REVERT: C 20 PHE cc_start: -0.5869 (OUTLIER) cc_final: -0.6134 (t80) REVERT: D 551 GLU cc_start: 0.7781 (tp30) cc_final: 0.6523 (mt-10) REVERT: F 20 PHE cc_start: -0.5889 (OUTLIER) cc_final: -0.6151 (t80) REVERT: F 94 ASP cc_start: 0.2453 (OUTLIER) cc_final: 0.2081 (t0) REVERT: G 551 GLU cc_start: 0.7800 (tp30) cc_final: 0.6542 (mt-10) REVERT: H 94 ASP cc_start: 0.2622 (OUTLIER) cc_final: 0.2259 (t0) outliers start: 57 outliers final: 46 residues processed: 262 average time/residue: 0.2426 time to fit residues: 97.0583 Evaluate side-chains 270 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 325 ARG Chi-restraints excluded: chain H residue 20 PHE Chi-restraints excluded: chain H residue 94 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 58 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 173 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 30.0000 chunk 52 optimal weight: 0.6980 chunk 186 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.246488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.146426 restraints weight = 62012.263| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.24 r_work: 0.3421 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16208 Z= 0.145 Angle : 0.474 5.890 21888 Z= 0.259 Chirality : 0.034 0.162 2444 Planarity : 0.003 0.039 2728 Dihedral : 5.663 47.532 2244 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.23 % Allowed : 17.93 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.19), residues: 1928 helix: 2.12 (0.13), residues: 1588 sheet: None (None), residues: 0 loop : -0.30 (0.39), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 366 TYR 0.006 0.001 TYR A 271 PHE 0.013 0.001 PHE A 171 TRP 0.006 0.001 TRP A 180 HIS 0.002 0.001 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (16208) covalent geometry : angle 0.47395 / 0.26 (21888) hydrogen bonds : bond 0.04336 / 2.85 ( 1233) hydrogen bonds : angle 4.68994 / 3.49 ( 3687) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 289 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 236 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 GLU cc_start: 0.7854 (tp30) cc_final: 0.6623 (mt-10) REVERT: B 551 GLU cc_start: 0.7836 (tp30) cc_final: 0.6610 (mt-10) REVERT: C 20 PHE cc_start: -0.5839 (OUTLIER) cc_final: -0.6111 (t80) REVERT: D 551 GLU cc_start: 0.7829 (tp30) cc_final: 0.6605 (mt-10) REVERT: F 20 PHE cc_start: -0.5900 (OUTLIER) cc_final: -0.6170 (t80) REVERT: G 551 GLU cc_start: 0.7844 (tp30) cc_final: 0.6626 (mt-10) outliers start: 53 outliers final: 49 residues processed: 264 average time/residue: 0.2355 time to fit residues: 96.9687 Evaluate side-chains 283 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 232 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 325 ARG Chi-restraints excluded: chain H residue 20 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 77 optimal weight: 20.0000 chunk 168 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 87 optimal weight: 30.0000 chunk 151 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.246242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.146001 restraints weight = 61889.496| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.22 r_work: 0.3401 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16208 Z= 0.165 Angle : 0.487 5.394 21888 Z= 0.267 Chirality : 0.034 0.170 2444 Planarity : 0.003 0.038 2728 Dihedral : 5.521 43.477 2244 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.29 % Allowed : 17.93 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.19), residues: 1928 helix: 2.18 (0.13), residues: 1584 sheet: None (None), residues: 0 loop : -0.32 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 366 TYR 0.006 0.001 TYR A 129 PHE 0.017 0.001 PHE G 197 TRP 0.008 0.001 TRP A 378 HIS 0.002 0.001 HIS A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (16208) covalent geometry : angle 0.48721 / 0.27 (21888) hydrogen bonds : bond 0.04365 / 2.87 ( 1233) hydrogen bonds : angle 4.68297 / 3.48 ( 3687) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3856 Ramachandran restraints generated. 1928 Oldfield, 0 Emsley, 1928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 228 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 GLU cc_start: 0.7893 (tp30) cc_final: 0.6642 (mt-10) REVERT: B 551 GLU cc_start: 0.7868 (tp30) cc_final: 0.6633 (mt-10) REVERT: C 20 PHE cc_start: -0.5799 (OUTLIER) cc_final: -0.6081 (t80) REVERT: D 551 GLU cc_start: 0.7846 (tp30) cc_final: 0.6597 (mt-10) REVERT: F 20 PHE cc_start: -0.5821 (OUTLIER) cc_final: -0.6102 (t80) REVERT: G 551 GLU cc_start: 0.7839 (tp30) cc_final: 0.6647 (mt-10) outliers start: 54 outliers final: 50 residues processed: 258 average time/residue: 0.2380 time to fit residues: 95.5004 Evaluate side-chains 280 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 228 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 TYR Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain E residue 20 PHE Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 203 CYS Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 20 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 113 ASN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 203 CYS Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 20 PHE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 108 TYR Chi-restraints excluded: chain G residue 113 ASN Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 203 CYS Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 325 ARG Chi-restraints excluded: chain H residue 20 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 157 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 35 optimal weight: 30.0000 chunk 155 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 183 optimal weight: 40.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.247222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.147052 restraints weight = 62174.549| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.25 r_work: 0.3443 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16208 Z= 0.141 Angle : 0.474 5.231 21888 Z= 0.260 Chirality : 0.033 0.170 2444 Planarity : 0.003 0.035 2728 Dihedral : 5.380 43.168 2244 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.05 % Allowed : 18.48 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.20), residues: 1928 helix: 2.17 (0.13), residues: 1588 sheet: None (None), residues: 0 loop : -0.26 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 366 TYR 0.018 0.001 TYR B 544 PHE 0.014 0.001 PHE G 363 TRP 0.006 0.001 TRP A 180 HIS 0.002 0.000 HIS G 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (16208) covalent geometry : angle 0.47384 / 0.26 (21888) hydrogen bonds : bond 0.04269 / 2.81 ( 1233) hydrogen bonds : angle 4.62868 / 3.44 ( 3687) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10520.99 seconds wall clock time: 178 minutes 10.96 seconds (10690.96 seconds total)