Starting phenix.real_space_refine on Sat Jul 4 01:24:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4s_41893/07_2026/8u4s_41893.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4s_41893/07_2026/8u4s_41893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u4s_41893/07_2026/8u4s_41893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4s_41893/07_2026/8u4s_41893.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u4s_41893/07_2026/8u4s_41893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4s_41893/07_2026/8u4s_41893.map" } resolution = 3.35 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6024 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 69 5.16 5 C 8316 2.51 5 N 2064 2.21 5 O 2232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 12684 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 856 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 976 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "R" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2297 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 10, 'TRANS': 273} Chain: "R" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 99 Unusual residues: {'CLR': 2, 'D21': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Restraints were copied for chains: A, E, B, F, C, G Time building chain proxies: 1.90, per 1000 atoms: 0.15 Number of scatterers: 12684 At special positions: 0 Unit cell: (105.4, 107.1, 107.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 69 16.00 P 3 15.00 O 2232 8.00 N 2064 7.00 C 8316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 28 " - pdb=" SG CYS R 274 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 93 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS G 28 " - pdb=" SG CYS G 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 109 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS G 109 " - pdb=" SG CYS G 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 489.4 milliseconds 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2892 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 15 sheets defined 46.6% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.598A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.638A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'R' and resid 33 through 64 removed outlier: 3.761A pdb=" N ILE R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) Proline residue: R 42 - end of helix Processing helix chain 'R' and resid 71 through 90 removed outlier: 3.535A pdb=" N LYS R 75 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR R 76 " --> pdb=" O MET R 72 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR R 90 " --> pdb=" O LEU R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 100 Processing helix chain 'R' and resid 104 through 139 removed outlier: 4.282A pdb=" N LEU R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU R 120 " --> pdb=" O TYR R 116 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR R 121 " --> pdb=" O THR R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 154 Processing helix chain 'R' and resid 154 through 167 removed outlier: 4.033A pdb=" N VAL R 158 " --> pdb=" O LYS R 154 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE R 162 " --> pdb=" O VAL R 158 " (cutoff:3.500A) Proline residue: R 163 - end of helix Processing helix chain 'R' and resid 168 through 174 Processing helix chain 'R' and resid 192 through 227 removed outlier: 3.541A pdb=" N VAL R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.800A pdb=" N CYS R 220 " --> pdb=" O LEU R 216 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER R 227 " --> pdb=" O ILE R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 267 Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 274 through 291 Processing helix chain 'R' and resid 292 through 302 removed outlier: 4.198A pdb=" N CYS R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.597A pdb=" N SER B 31 " --> pdb=" O THR B 28 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.638A pdb=" N ASP B 90 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 91' Processing helix chain 'C' and resid 33 through 64 removed outlier: 3.762A pdb=" N ILE C 39 " --> pdb=" O ASN C 35 " (cutoff:3.500A) Proline residue: C 42 - end of helix Processing helix chain 'C' and resid 71 through 90 removed outlier: 3.536A pdb=" N LYS C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 100 Processing helix chain 'C' and resid 104 through 139 removed outlier: 4.282A pdb=" N LEU C 108 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 120 " --> pdb=" O TYR C 116 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 154 Processing helix chain 'C' and resid 154 through 167 removed outlier: 4.033A pdb=" N VAL C 158 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Proline residue: C 163 - end of helix Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 192 through 227 removed outlier: 3.542A pdb=" N VAL C 196 " --> pdb=" O ASN C 192 " (cutoff:3.500A) Proline residue: C 211 - end of helix removed outlier: 3.801A pdb=" N CYS C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 227 " --> pdb=" O ILE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 267 Proline residue: C 254 - end of helix Processing helix chain 'C' and resid 274 through 291 Processing helix chain 'C' and resid 292 through 302 removed outlier: 4.198A pdb=" N CYS C 296 " --> pdb=" O PHE C 292 " (cutoff:3.500A) Proline residue: C 299 - end of helix Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.598A pdb=" N SER F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.638A pdb=" N ASP F 90 " --> pdb=" O ARG F 87 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 87 through 91' Processing helix chain 'G' and resid 33 through 64 removed outlier: 3.762A pdb=" N ILE G 39 " --> pdb=" O ASN G 35 " (cutoff:3.500A) Proline residue: G 42 - end of helix Processing helix chain 'G' and resid 71 through 90 removed outlier: 3.535A pdb=" N LYS G 75 " --> pdb=" O SER G 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR G 76 " --> pdb=" O MET G 72 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR G 90 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 100 Processing helix chain 'G' and resid 104 through 139 removed outlier: 4.282A pdb=" N LEU G 108 " --> pdb=" O PHE G 104 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU G 120 " --> pdb=" O TYR G 116 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR G 121 " --> pdb=" O THR G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 154 Processing helix chain 'G' and resid 154 through 167 removed outlier: 4.034A pdb=" N VAL G 158 " --> pdb=" O LYS G 154 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE G 162 " --> pdb=" O VAL G 158 " (cutoff:3.500A) Proline residue: G 163 - end of helix Processing helix chain 'G' and resid 168 through 174 Processing helix chain 'G' and resid 192 through 227 removed outlier: 3.542A pdb=" N VAL G 196 " --> pdb=" O ASN G 192 " (cutoff:3.500A) Proline residue: G 211 - end of helix removed outlier: 3.801A pdb=" N CYS G 220 " --> pdb=" O LEU G 216 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 267 Proline residue: G 254 - end of helix Processing helix chain 'G' and resid 274 through 291 Processing helix chain 'G' and resid 292 through 302 removed outlier: 4.198A pdb=" N CYS G 296 " --> pdb=" O PHE G 292 " (cutoff:3.500A) Proline residue: G 299 - end of helix Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.926A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 11 removed outlier: 4.163A pdb=" N LEU L 38 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TYR L 54 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS L 55 " --> pdb=" O ASN L 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.826A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 175 through 180 removed outlier: 3.525A pdb=" N ASN R 176 " --> pdb=" O ASP R 187 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP R 187 " --> pdb=" O ASN R 176 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA R 180 " --> pdb=" O ARG R 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 5 through 7 removed outlier: 3.926A pdb=" N THR A 5 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A 24 " --> pdb=" O THR A 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 10 through 11 removed outlier: 4.163A pdb=" N LEU A 38 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TYR A 54 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP A 40 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 55 " --> pdb=" O ASN A 58 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.826A pdb=" N ILE B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TRP B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 48 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 175 through 180 removed outlier: 3.525A pdb=" N ASN C 176 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP C 187 " --> pdb=" O ASN C 176 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 180 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.926A pdb=" N THR E 5 " --> pdb=" O ARG E 24 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG E 24 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 11 removed outlier: 4.163A pdb=" N LEU E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TYR E 54 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS E 55 " --> pdb=" O ASN E 58 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.826A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET F 48 " --> pdb=" O TRP F 36 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 175 through 180 removed outlier: 3.525A pdb=" N ASN G 176 " --> pdb=" O ASP G 187 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP G 187 " --> pdb=" O ASN G 176 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA G 180 " --> pdb=" O ARG G 183 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3695 1.34 - 1.47: 3563 1.47 - 1.59: 5663 1.59 - 1.72: 0 1.72 - 1.85: 102 Bond restraints: 13023 Sorted by residual: bond pdb=" O22 D21 R 702 " pdb=" P23 D21 R 702 " ideal model delta sigma weight residual 1.723 1.853 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" O22 D21 G 702 " pdb=" P23 D21 G 702 " ideal model delta sigma weight residual 1.723 1.853 -0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" O22 D21 C 702 " pdb=" P23 D21 C 702 " ideal model delta sigma weight residual 1.723 1.853 -0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" C20 D21 G 702 " pdb=" C21 D21 G 702 " ideal model delta sigma weight residual 1.525 1.582 -0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" C21 D21 R 702 " pdb=" O22 D21 R 702 " ideal model delta sigma weight residual 1.389 1.332 0.057 2.00e-02 2.50e+03 8.09e+00 ... (remaining 13018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 17581 4.15 - 8.30: 116 8.30 - 12.45: 9 12.45 - 16.60: 0 16.60 - 20.75: 3 Bond angle restraints: 17709 Sorted by residual: angle pdb=" CB MET F 113 " pdb=" CG MET F 113 " pdb=" SD MET F 113 " ideal model delta sigma weight residual 112.70 133.45 -20.75 3.00e+00 1.11e-01 4.78e+01 angle pdb=" CB MET H 113 " pdb=" CG MET H 113 " pdb=" SD MET H 113 " ideal model delta sigma weight residual 112.70 133.43 -20.73 3.00e+00 1.11e-01 4.77e+01 angle pdb=" CB MET B 113 " pdb=" CG MET B 113 " pdb=" SD MET B 113 " ideal model delta sigma weight residual 112.70 133.40 -20.70 3.00e+00 1.11e-01 4.76e+01 angle pdb=" CA MET B 113 " pdb=" CB MET B 113 " pdb=" CG MET B 113 " ideal model delta sigma weight residual 114.10 123.20 -9.10 2.00e+00 2.50e-01 2.07e+01 angle pdb=" CA MET H 113 " pdb=" CB MET H 113 " pdb=" CG MET H 113 " ideal model delta sigma weight residual 114.10 123.15 -9.05 2.00e+00 2.50e-01 2.05e+01 ... (remaining 17704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.32: 7618 30.32 - 60.63: 287 60.63 - 90.94: 24 90.94 - 121.26: 3 121.26 - 151.57: 6 Dihedral angle restraints: 7938 sinusoidal: 3408 harmonic: 4530 Sorted by residual: dihedral pdb=" CB CYS C 28 " pdb=" SG CYS C 28 " pdb=" SG CYS C 274 " pdb=" CB CYS C 274 " ideal model delta sinusoidal sigma weight residual 93.00 168.19 -75.19 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS R 28 " pdb=" SG CYS R 28 " pdb=" SG CYS R 274 " pdb=" CB CYS R 274 " ideal model delta sinusoidal sigma weight residual 93.00 168.17 -75.17 1 1.00e+01 1.00e-02 7.14e+01 dihedral pdb=" CB CYS G 28 " pdb=" SG CYS G 28 " pdb=" SG CYS G 274 " pdb=" CB CYS G 274 " ideal model delta sinusoidal sigma weight residual 93.00 168.14 -75.14 1 1.00e+01 1.00e-02 7.14e+01 ... (remaining 7935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1762 0.077 - 0.155: 203 0.155 - 0.232: 3 0.232 - 0.309: 18 0.309 - 0.386: 6 Chirality restraints: 1992 Sorted by residual: chirality pdb=" C17 CLR G 701 " pdb=" C13 CLR G 701 " pdb=" C16 CLR G 701 " pdb=" C20 CLR G 701 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" C17 CLR C 701 " pdb=" C13 CLR C 701 " pdb=" C16 CLR C 701 " pdb=" C20 CLR C 701 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C17 CLR R 701 " pdb=" C13 CLR R 701 " pdb=" C16 CLR R 701 " pdb=" C20 CLR R 701 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 1989 not shown) Planarity restraints: 2151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 44 " 0.055 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO L 45 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO L 45 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO L 45 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 44 " -0.055 5.00e-02 4.00e+02 8.31e-02 1.10e+01 pdb=" N PRO E 45 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO E 45 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 45 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 44 " -0.055 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO A 45 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " -0.046 5.00e-02 4.00e+02 ... (remaining 2148 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 937 2.74 - 3.28: 12363 3.28 - 3.82: 20074 3.82 - 4.36: 22905 4.36 - 4.90: 41811 Nonbonded interactions: 98090 Sorted by model distance: nonbonded pdb=" OH TYR A 54 " pdb=" OD2 ASP C 182 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR L 54 " pdb=" OD2 ASP R 182 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR E 54 " pdb=" OD2 ASP G 182 " model vdw 2.202 3.040 nonbonded pdb=" OG SER L 25 " pdb=" O GLN L 27 " model vdw 2.235 3.040 nonbonded pdb=" OG SER A 25 " pdb=" O GLN A 27 " model vdw 2.236 3.040 ... (remaining 98085 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: 0.03 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'H' selection = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'R' selection = chain 'C' selection = chain 'G' } 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: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.220 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 0.005 0.130 13035 Z= 0.236 Angle : 0.829 20.751 17733 Z= 0.387 Chirality : 0.056 0.386 1992 Planarity : 0.006 0.083 2151 Dihedral : 15.847 151.574 5010 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.67 % Allowed : 1.11 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.22), residues: 1539 helix: 1.92 (0.21), residues: 651 sheet: 0.13 (0.27), residues: 348 loop : -1.74 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 30 TYR 0.014 0.001 TYR A 31 PHE 0.021 0.001 PHE A 90 TRP 0.013 0.001 TRP C 195 HIS 0.002 0.001 HIS G 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.24 (13023) covalent geometry : angle 0.82762 / 0.39 (17709) SS BOND : bond 0.00417 / 0.30 ( 12) SS BOND : angle 1.68165 / 1.18 ( 24) hydrogen bonds : bond 0.10197 / 7.02 ( 672) hydrogen bonds : angle 5.22721 / 3.62 ( 1881) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 297 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: H 58 ARG cc_start: 0.7843 (pmt-80) cc_final: 0.7348 (pmt-80) REVERT: R 153 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7895 (tp30) REVERT: R 195 TRP cc_start: 0.7196 (m100) cc_final: 0.5974 (m-90) REVERT: R 205 MET cc_start: 0.7470 (tmm) cc_final: 0.7249 (tmm) REVERT: R 284 ILE cc_start: 0.8201 (mt) cc_final: 0.7877 (mt) REVERT: C 153 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8006 (tp30) REVERT: C 195 TRP cc_start: 0.7146 (m100) cc_final: 0.5994 (m-90) REVERT: F 58 ARG cc_start: 0.7767 (pmt-80) cc_final: 0.7243 (pmt-80) REVERT: G 153 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7907 (tp30) REVERT: G 195 TRP cc_start: 0.7263 (m100) cc_final: 0.5967 (m-90) outliers start: 9 outliers final: 6 residues processed: 297 average time/residue: 0.1056 time to fit residues: 44.3347 Evaluate side-chains 260 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 251 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain R residue 153 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain G residue 153 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113214 restraints weight = 18382.040| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.15 r_work: 0.3222 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13035 Z= 0.177 Angle : 0.613 6.449 17733 Z= 0.321 Chirality : 0.046 0.165 1992 Planarity : 0.005 0.048 2151 Dihedral : 13.051 157.778 2250 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.14 % Allowed : 10.42 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.22), residues: 1539 helix: 1.85 (0.21), residues: 663 sheet: 0.14 (0.28), residues: 354 loop : -1.57 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 188 TYR 0.011 0.001 TYR F 111 PHE 0.014 0.001 PHE G 29 TRP 0.012 0.001 TRP B 47 HIS 0.005 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (13023) covalent geometry : angle 0.61009 / 0.32 (17709) SS BOND : bond 0.00405 / 0.29 ( 12) SS BOND : angle 1.60248 / 1.12 ( 24) hydrogen bonds : bond 0.05073 / 3.45 ( 672) hydrogen bonds : angle 4.88728 / 3.38 ( 1881) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 274 time to evaluate : 0.379 Fit side-chains REVERT: L 60 ASP cc_start: 0.8666 (p0) cc_final: 0.8276 (p0) REVERT: H 58 ARG cc_start: 0.8299 (pmt-80) cc_final: 0.7969 (pmt-80) REVERT: H 106 ASN cc_start: 0.8345 (m110) cc_final: 0.7699 (m110) REVERT: R 65 TYR cc_start: 0.8731 (t80) cc_final: 0.8428 (t80) REVERT: R 183 ARG cc_start: 0.7913 (ttt90) cc_final: 0.7675 (ttt90) REVERT: R 195 TRP cc_start: 0.7484 (m100) cc_final: 0.6410 (m-90) REVERT: A 60 ASP cc_start: 0.8636 (p0) cc_final: 0.8326 (p0) REVERT: A 79 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8486 (ptpp) REVERT: B 57 ASN cc_start: 0.8808 (m110) cc_final: 0.8498 (m-40) REVERT: B 106 ASN cc_start: 0.8324 (m110) cc_final: 0.8024 (m-40) REVERT: B 111 TYR cc_start: 0.8348 (m-80) cc_final: 0.8126 (m-80) REVERT: C 195 TRP cc_start: 0.7644 (m100) cc_final: 0.6621 (m-90) REVERT: C 205 MET cc_start: 0.8509 (tmm) cc_final: 0.8152 (tmm) REVERT: E 60 ASP cc_start: 0.8543 (p0) cc_final: 0.8315 (p0) REVERT: F 58 ARG cc_start: 0.8292 (pmt-80) cc_final: 0.7803 (pmt-80) REVERT: F 81 MET cc_start: 0.8154 (tmm) cc_final: 0.7925 (ttt) REVERT: F 106 ASN cc_start: 0.8400 (m110) cc_final: 0.7923 (m-40) REVERT: F 111 TYR cc_start: 0.8277 (m-80) cc_final: 0.8067 (m-10) REVERT: G 195 TRP cc_start: 0.7529 (m100) cc_final: 0.6428 (m-90) REVERT: G 253 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8779 (tt) outliers start: 29 outliers final: 14 residues processed: 282 average time/residue: 0.1020 time to fit residues: 41.2668 Evaluate side-chains 276 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 260 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 143 ASN Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 253 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 150 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 134 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 57 ASN F 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112444 restraints weight = 18554.822| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.16 r_work: 0.3211 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13035 Z= 0.153 Angle : 0.589 8.636 17733 Z= 0.307 Chirality : 0.044 0.155 1992 Planarity : 0.004 0.039 2151 Dihedral : 12.664 156.949 2232 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.14 % Allowed : 13.45 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.22), residues: 1539 helix: 1.76 (0.21), residues: 663 sheet: 0.19 (0.28), residues: 354 loop : -1.56 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 188 TYR 0.010 0.001 TYR R 302 PHE 0.013 0.001 PHE G 29 TRP 0.010 0.001 TRP F 47 HIS 0.004 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (13023) covalent geometry : angle 0.58525 / 0.31 (17709) SS BOND : bond 0.00478 / 0.34 ( 12) SS BOND : angle 1.78084 / 1.17 ( 24) hydrogen bonds : bond 0.04752 / 3.25 ( 672) hydrogen bonds : angle 4.78082 / 3.31 ( 1881) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 278 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: L 60 ASP cc_start: 0.8706 (p0) cc_final: 0.8272 (p0) REVERT: H 106 ASN cc_start: 0.8403 (m110) cc_final: 0.7847 (m110) REVERT: R 68 LYS cc_start: 0.8153 (mttt) cc_final: 0.7894 (mttm) REVERT: R 205 MET cc_start: 0.8321 (tmm) cc_final: 0.8091 (tpp) REVERT: R 253 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8716 (tt) REVERT: A 60 ASP cc_start: 0.8728 (p0) cc_final: 0.8417 (p0) REVERT: A 79 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8520 (ptpp) REVERT: B 106 ASN cc_start: 0.8409 (m110) cc_final: 0.8048 (m-40) REVERT: B 111 TYR cc_start: 0.8332 (m-80) cc_final: 0.8095 (m-80) REVERT: C 195 TRP cc_start: 0.7689 (m100) cc_final: 0.6680 (m-90) REVERT: C 205 MET cc_start: 0.8470 (tmm) cc_final: 0.8213 (tpp) REVERT: F 81 MET cc_start: 0.8168 (tmm) cc_final: 0.7937 (ttt) REVERT: F 106 ASN cc_start: 0.8431 (m-40) cc_final: 0.8135 (m-40) REVERT: F 111 TYR cc_start: 0.8270 (m-80) cc_final: 0.8059 (m-10) REVERT: F 113 MET cc_start: 0.7997 (tpp) cc_final: 0.7661 (mmt) REVERT: G 150 LEU cc_start: 0.9028 (tt) cc_final: 0.8798 (tp) REVERT: G 195 TRP cc_start: 0.7613 (m100) cc_final: 0.6632 (m-90) REVERT: G 253 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8785 (tt) outliers start: 29 outliers final: 18 residues processed: 294 average time/residue: 0.0921 time to fit residues: 39.4274 Evaluate side-chains 283 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 262 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 143 ASN Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 297 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 68 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 75 optimal weight: 0.4980 chunk 63 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 108 optimal weight: 0.4980 chunk 115 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.106616 restraints weight = 18601.225| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.37 r_work: 0.3122 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13035 Z= 0.165 Angle : 0.608 8.254 17733 Z= 0.314 Chirality : 0.045 0.175 1992 Planarity : 0.004 0.039 2151 Dihedral : 12.737 157.228 2229 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.18 % Allowed : 15.52 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.22), residues: 1539 helix: 1.78 (0.21), residues: 648 sheet: 0.19 (0.28), residues: 354 loop : -1.64 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 183 TYR 0.009 0.001 TYR B 32 PHE 0.012 0.001 PHE C 29 TRP 0.009 0.001 TRP F 47 HIS 0.005 0.001 HIS G 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (13023) covalent geometry : angle 0.60481 / 0.31 (17709) SS BOND : bond 0.00413 / 0.30 ( 12) SS BOND : angle 1.86744 / 1.19 ( 24) hydrogen bonds : bond 0.04889 / 3.33 ( 672) hydrogen bonds : angle 4.75935 / 3.29 ( 1881) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 0.401 Fit side-chains REVERT: L 59 ARG cc_start: 0.8688 (ptt-90) cc_final: 0.8213 (ptt90) REVERT: L 60 ASP cc_start: 0.8679 (p0) cc_final: 0.8335 (p0) REVERT: H 106 ASN cc_start: 0.8370 (m-40) cc_final: 0.7774 (m110) REVERT: R 65 TYR cc_start: 0.8686 (t80) cc_final: 0.8367 (t80) REVERT: R 68 LYS cc_start: 0.8153 (mttt) cc_final: 0.7895 (mttm) REVERT: A 79 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8416 (ptpp) REVERT: B 57 ASN cc_start: 0.8856 (m110) cc_final: 0.8461 (m-40) REVERT: B 106 ASN cc_start: 0.8399 (m110) cc_final: 0.8097 (m-40) REVERT: C 272 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.6604 (mp10) REVERT: F 111 TYR cc_start: 0.8223 (m-80) cc_final: 0.7993 (m-10) REVERT: F 113 MET cc_start: 0.8060 (tpp) cc_final: 0.7576 (mmt) REVERT: G 195 TRP cc_start: 0.7655 (m100) cc_final: 0.6588 (m-90) REVERT: G 253 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8698 (tt) REVERT: G 272 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.6666 (mp10) outliers start: 43 outliers final: 28 residues processed: 302 average time/residue: 0.0996 time to fit residues: 43.9498 Evaluate side-chains 300 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 268 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 143 ASN Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 297 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 2 optimal weight: 0.2980 chunk 129 optimal weight: 0.7980 chunk 117 optimal weight: 0.0370 chunk 107 optimal weight: 5.9990 chunk 138 optimal weight: 0.0010 chunk 89 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 overall best weight: 0.4264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.106327 restraints weight = 18514.095| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.63 r_work: 0.3122 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13035 Z= 0.115 Angle : 0.559 7.856 17733 Z= 0.289 Chirality : 0.043 0.172 1992 Planarity : 0.004 0.037 2151 Dihedral : 12.328 156.081 2229 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.37 % Allowed : 17.15 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.22), residues: 1539 helix: 1.74 (0.21), residues: 666 sheet: 0.10 (0.28), residues: 360 loop : -1.59 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 183 TYR 0.010 0.001 TYR G 302 PHE 0.008 0.001 PHE G 87 TRP 0.008 0.001 TRP C 195 HIS 0.003 0.001 HIS R 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (13023) covalent geometry : angle 0.55693 / 0.29 (17709) SS BOND : bond 0.00346 / 0.24 ( 12) SS BOND : angle 1.48008 / 0.95 ( 24) hydrogen bonds : bond 0.04127 / 2.81 ( 672) hydrogen bonds : angle 4.61465 / 3.19 ( 1881) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 264 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: L 59 ARG cc_start: 0.8365 (ptt-90) cc_final: 0.7782 (ptt90) REVERT: H 106 ASN cc_start: 0.8199 (m-40) cc_final: 0.7634 (m110) REVERT: H 113 MET cc_start: 0.8118 (mmm) cc_final: 0.7875 (tpp) REVERT: A 59 ARG cc_start: 0.8188 (ptt90) cc_final: 0.7647 (ptt90) REVERT: B 106 ASN cc_start: 0.8095 (m110) cc_final: 0.7811 (m-40) REVERT: F 113 MET cc_start: 0.7997 (tpp) cc_final: 0.7703 (mmt) REVERT: G 195 TRP cc_start: 0.7214 (m100) cc_final: 0.5912 (m-90) REVERT: G 253 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8282 (tt) outliers start: 32 outliers final: 23 residues processed: 279 average time/residue: 0.0951 time to fit residues: 38.1473 Evaluate side-chains 276 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain R residue 143 ASN Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 297 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 126 optimal weight: 0.0980 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099580 restraints weight = 18622.543| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.62 r_work: 0.3024 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13035 Z= 0.210 Angle : 0.643 8.358 17733 Z= 0.333 Chirality : 0.046 0.196 1992 Planarity : 0.004 0.039 2151 Dihedral : 12.596 157.954 2229 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.70 % Allowed : 17.15 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.22), residues: 1539 helix: 1.54 (0.21), residues: 666 sheet: 0.21 (0.28), residues: 354 loop : -1.60 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 188 TYR 0.011 0.001 TYR F 32 PHE 0.011 0.001 PHE C 29 TRP 0.015 0.001 TRP B 47 HIS 0.007 0.001 HIS R 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.21 (13023) covalent geometry : angle 0.63865 / 0.33 (17709) SS BOND : bond 0.00474 / 0.35 ( 12) SS BOND : angle 2.01792 / 1.28 ( 24) hydrogen bonds : bond 0.05227 / 3.56 ( 672) hydrogen bonds : angle 4.81365 / 3.32 ( 1881) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 271 time to evaluate : 0.390 Fit side-chains REVERT: L 59 ARG cc_start: 0.8540 (ptt-90) cc_final: 0.7918 (ptt90) REVERT: H 106 ASN cc_start: 0.8397 (m-40) cc_final: 0.7857 (m110) REVERT: R 65 TYR cc_start: 0.8580 (t80) cc_final: 0.8249 (t80) REVERT: R 272 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.6256 (mp10) REVERT: A 79 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8135 (ptpp) REVERT: B 57 ASN cc_start: 0.8804 (m110) cc_final: 0.8260 (m110) REVERT: B 106 ASN cc_start: 0.8175 (m-40) cc_final: 0.7941 (m-40) REVERT: B 111 TYR cc_start: 0.8249 (m-80) cc_final: 0.8043 (m-80) REVERT: C 272 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.6339 (mp10) REVERT: F 113 MET cc_start: 0.8195 (tpp) cc_final: 0.7627 (mmt) REVERT: G 195 TRP cc_start: 0.7293 (m100) cc_final: 0.5972 (m-90) REVERT: G 205 MET cc_start: 0.7690 (tmm) cc_final: 0.7218 (tpp) REVERT: G 253 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8374 (tt) REVERT: G 272 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.6621 (mp10) outliers start: 50 outliers final: 34 residues processed: 292 average time/residue: 0.0976 time to fit residues: 41.3522 Evaluate side-chains 302 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 263 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 272 GLN Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 204 ILE Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 297 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 120 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.127579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100995 restraints weight = 18573.210| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.61 r_work: 0.3047 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13035 Z= 0.161 Angle : 0.618 9.171 17733 Z= 0.316 Chirality : 0.045 0.209 1992 Planarity : 0.004 0.039 2151 Dihedral : 12.283 157.562 2229 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.25 % Allowed : 18.55 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.22), residues: 1539 helix: 1.53 (0.21), residues: 666 sheet: 0.21 (0.28), residues: 354 loop : -1.58 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 188 TYR 0.011 0.001 TYR A 54 PHE 0.008 0.001 PHE G 29 TRP 0.011 0.001 TRP B 47 HIS 0.005 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (13023) covalent geometry : angle 0.61548 / 0.31 (17709) SS BOND : bond 0.00400 / 0.30 ( 12) SS BOND : angle 1.66894 / 1.08 ( 24) hydrogen bonds : bond 0.04816 / 3.28 ( 672) hydrogen bonds : angle 4.76189 / 3.28 ( 1881) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 271 time to evaluate : 0.352 Fit side-chains REVERT: L 59 ARG cc_start: 0.8446 (ptt-90) cc_final: 0.7835 (ptt90) REVERT: H 106 ASN cc_start: 0.8413 (m-40) cc_final: 0.7784 (m110) REVERT: R 65 TYR cc_start: 0.8517 (t80) cc_final: 0.8201 (t80) REVERT: R 253 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8345 (tt) REVERT: R 272 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.6234 (mp10) REVERT: A 59 ARG cc_start: 0.8042 (ptt90) cc_final: 0.7450 (ptt90) REVERT: A 79 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8120 (ptpp) REVERT: B 57 ASN cc_start: 0.8821 (m110) cc_final: 0.8259 (m110) REVERT: B 91 THR cc_start: 0.8218 (t) cc_final: 0.8018 (t) REVERT: B 106 ASN cc_start: 0.8252 (m-40) cc_final: 0.7954 (m-40) REVERT: F 57 ASN cc_start: 0.8756 (m-40) cc_final: 0.8283 (m110) REVERT: F 113 MET cc_start: 0.8160 (tpp) cc_final: 0.7714 (mmt) REVERT: G 195 TRP cc_start: 0.7271 (m100) cc_final: 0.5989 (m-90) REVERT: G 205 MET cc_start: 0.7622 (tmm) cc_final: 0.7161 (tpp) REVERT: G 253 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8316 (tt) outliers start: 44 outliers final: 31 residues processed: 294 average time/residue: 0.1011 time to fit residues: 42.8382 Evaluate side-chains 299 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain R residue 143 ASN Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 272 GLN Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 297 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 48 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 chunk 18 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.127104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100455 restraints weight = 18500.753| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.60 r_work: 0.3040 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13035 Z= 0.168 Angle : 0.628 8.859 17733 Z= 0.321 Chirality : 0.045 0.216 1992 Planarity : 0.004 0.039 2151 Dihedral : 12.165 157.522 2229 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.40 % Allowed : 19.14 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.22), residues: 1539 helix: 1.50 (0.21), residues: 666 sheet: 0.20 (0.28), residues: 354 loop : -1.57 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 51 TYR 0.011 0.001 TYR A 54 PHE 0.010 0.001 PHE G 87 TRP 0.012 0.001 TRP B 47 HIS 0.005 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (13023) covalent geometry : angle 0.62489 / 0.32 (17709) SS BOND : bond 0.00398 / 0.29 ( 12) SS BOND : angle 1.85398 / 1.16 ( 24) hydrogen bonds : bond 0.04903 / 3.35 ( 672) hydrogen bonds : angle 4.75479 / 3.28 ( 1881) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 275 time to evaluate : 0.380 Fit side-chains REVERT: H 106 ASN cc_start: 0.8436 (m-40) cc_final: 0.7812 (m110) REVERT: R 65 TYR cc_start: 0.8538 (t80) cc_final: 0.8214 (t80) REVERT: R 253 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8346 (tt) REVERT: R 272 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.6177 (mp10) REVERT: A 59 ARG cc_start: 0.8073 (ptt90) cc_final: 0.7505 (ptt90) REVERT: A 79 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8120 (ptpp) REVERT: B 57 ASN cc_start: 0.8824 (m110) cc_final: 0.8273 (m110) REVERT: B 91 THR cc_start: 0.8222 (t) cc_final: 0.8005 (t) REVERT: B 106 ASN cc_start: 0.8331 (m-40) cc_final: 0.8073 (m110) REVERT: F 113 MET cc_start: 0.8162 (tpp) cc_final: 0.7664 (mmt) REVERT: G 149 LYS cc_start: 0.8280 (tptp) cc_final: 0.8028 (tmmt) REVERT: G 195 TRP cc_start: 0.7261 (m100) cc_final: 0.6011 (m-90) REVERT: G 205 MET cc_start: 0.7659 (tmm) cc_final: 0.7185 (tpp) REVERT: G 253 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8335 (tt) outliers start: 46 outliers final: 36 residues processed: 299 average time/residue: 0.0980 time to fit residues: 41.9921 Evaluate side-chains 308 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 268 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain R residue 143 ASN Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 272 GLN Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 105 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 134 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.129143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.102126 restraints weight = 19170.993| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.59 r_work: 0.3118 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13035 Z= 0.132 Angle : 0.600 8.437 17733 Z= 0.306 Chirality : 0.044 0.212 1992 Planarity : 0.004 0.038 2151 Dihedral : 11.772 156.166 2229 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.18 % Allowed : 19.81 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.22), residues: 1539 helix: 1.60 (0.21), residues: 666 sheet: 0.14 (0.28), residues: 357 loop : -1.53 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 188 TYR 0.012 0.001 TYR A 54 PHE 0.006 0.001 PHE C 29 TRP 0.008 0.001 TRP C 195 HIS 0.004 0.001 HIS R 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (13023) covalent geometry : angle 0.59806 / 0.31 (17709) SS BOND : bond 0.00338 / 0.24 ( 12) SS BOND : angle 1.53168 / 0.99 ( 24) hydrogen bonds : bond 0.04423 / 3.02 ( 672) hydrogen bonds : angle 4.65604 / 3.22 ( 1881) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 278 time to evaluate : 0.292 Fit side-chains REVERT: L 11 LEU cc_start: 0.7470 (tt) cc_final: 0.7073 (tp) REVERT: H 106 ASN cc_start: 0.8529 (m-40) cc_final: 0.8018 (m110) REVERT: R 65 TYR cc_start: 0.8610 (t80) cc_final: 0.8286 (t80) REVERT: R 253 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8462 (tt) REVERT: R 272 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.6301 (mp10) REVERT: A 11 LEU cc_start: 0.7524 (tt) cc_final: 0.7131 (tp) REVERT: A 59 ARG cc_start: 0.8160 (ptt90) cc_final: 0.7694 (ptt90) REVERT: B 57 ASN cc_start: 0.8889 (m110) cc_final: 0.8461 (m110) REVERT: B 106 ASN cc_start: 0.8481 (m-40) cc_final: 0.8281 (m110) REVERT: C 272 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.6292 (mp10) REVERT: F 57 ASN cc_start: 0.8841 (m-40) cc_final: 0.8378 (m110) REVERT: F 113 MET cc_start: 0.8109 (tpp) cc_final: 0.7800 (mmt) REVERT: G 149 LYS cc_start: 0.8419 (tptp) cc_final: 0.8208 (tmmt) REVERT: G 195 TRP cc_start: 0.7340 (m100) cc_final: 0.6190 (m-90) REVERT: G 205 MET cc_start: 0.7887 (tmm) cc_final: 0.7375 (tpp) REVERT: G 253 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8532 (tt) outliers start: 43 outliers final: 34 residues processed: 300 average time/residue: 0.1028 time to fit residues: 44.3708 Evaluate side-chains 308 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 270 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 143 ASN Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 HIS Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 272 GLN Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 106 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.128690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101222 restraints weight = 19228.857| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.73 r_work: 0.3094 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13035 Z= 0.134 Angle : 0.612 9.890 17733 Z= 0.308 Chirality : 0.044 0.210 1992 Planarity : 0.004 0.038 2151 Dihedral : 11.648 155.778 2229 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.18 % Allowed : 20.10 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.22), residues: 1539 helix: 1.62 (0.21), residues: 666 sheet: 0.14 (0.28), residues: 357 loop : -1.54 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 188 TYR 0.011 0.001 TYR A 54 PHE 0.009 0.001 PHE C 87 TRP 0.016 0.001 TRP H 36 HIS 0.003 0.001 HIS C 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (13023) covalent geometry : angle 0.60949 / 0.31 (17709) SS BOND : bond 0.00340 / 0.24 ( 12) SS BOND : angle 1.53760 / 1.00 ( 24) hydrogen bonds : bond 0.04417 / 3.01 ( 672) hydrogen bonds : angle 4.62898 / 3.20 ( 1881) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3078 Ramachandran restraints generated. 1539 Oldfield, 0 Emsley, 1539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 275 time to evaluate : 0.299 Fit side-chains REVERT: L 11 LEU cc_start: 0.7447 (tt) cc_final: 0.7059 (tp) REVERT: H 106 ASN cc_start: 0.8505 (m-40) cc_final: 0.7935 (m110) REVERT: R 65 TYR cc_start: 0.8612 (t80) cc_final: 0.8304 (t80) REVERT: R 272 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.6273 (mp10) REVERT: A 11 LEU cc_start: 0.7493 (tt) cc_final: 0.7127 (tp) REVERT: A 59 ARG cc_start: 0.8180 (ptt90) cc_final: 0.7708 (ptt90) REVERT: B 57 ASN cc_start: 0.8885 (m110) cc_final: 0.8438 (m110) REVERT: C 272 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.6304 (mp10) REVERT: F 57 ASN cc_start: 0.8836 (m-40) cc_final: 0.8369 (m110) REVERT: F 113 MET cc_start: 0.8139 (tpp) cc_final: 0.7816 (mmt) REVERT: G 149 LYS cc_start: 0.8382 (tptp) cc_final: 0.8162 (tmmt) REVERT: G 150 LEU cc_start: 0.8791 (tt) cc_final: 0.8547 (tp) REVERT: G 195 TRP cc_start: 0.7323 (m100) cc_final: 0.6196 (m-90) REVERT: G 205 MET cc_start: 0.7887 (tmm) cc_final: 0.7379 (tpp) outliers start: 43 outliers final: 39 residues processed: 300 average time/residue: 0.0971 time to fit residues: 41.6537 Evaluate side-chains 312 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 271 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 143 ASN Chi-restraints excluded: chain R residue 156 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 HIS Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 272 GLN Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain E residue 17 GLN Chi-restraints excluded: chain E residue 39 ASN Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 65 GLN Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain G residue 228 HIS Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 274 CYS Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 87 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 0.0670 chunk 28 optimal weight: 0.0870 chunk 145 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 GLN B 106 ASN E 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.102166 restraints weight = 19148.656| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.73 r_work: 0.3107 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13035 Z= 0.128 Angle : 0.596 9.461 17733 Z= 0.303 Chirality : 0.043 0.204 1992 Planarity : 0.004 0.038 2151 Dihedral : 11.459 155.104 2229 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.03 % Allowed : 20.55 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1539 helix: 1.63 (0.21), residues: 666 sheet: 0.16 (0.28), residues: 357 loop : -1.55 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 188 TYR 0.011 0.001 TYR A 54 PHE 0.007 0.001 PHE G 29 TRP 0.015 0.001 TRP H 36 HIS 0.003 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (13023) covalent geometry : angle 0.59385 / 0.30 (17709) SS BOND : bond 0.00326 / 0.24 ( 12) SS BOND : angle 1.50958 / 0.97 ( 24) hydrogen bonds : bond 0.04269 / 2.91 ( 672) hydrogen bonds : angle 4.59367 / 3.18 ( 1881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2338.48 seconds wall clock time: 40 minutes 59.28 seconds (2459.28 seconds total)