Starting phenix.real_space_refine on Thu Feb 5 21:52:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r2s_53538/02_2026/9r2s_53538.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r2s_53538/02_2026/9r2s_53538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r2s_53538/02_2026/9r2s_53538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r2s_53538/02_2026/9r2s_53538.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r2s_53538/02_2026/9r2s_53538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r2s_53538/02_2026/9r2s_53538.map" } resolution = 2.68 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= -0.005 sd= 0.413 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 12572 2.51 5 N 3404 2.21 5 O 3921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19981 Number of models: 1 Model: "" Number of chains: 14 Chain: "Pb" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1468 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain: "Pe" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1443 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Pa" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1468 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain: "Pc" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1459 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain: "Pd" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1468 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain: "Pg" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1403 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain breaks: 1 Chain: "Po" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1377 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 1 Chain: "Pf" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1468 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain: "Pq" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1377 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 1 Chain: "Pi" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1402 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "Pn" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1413 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Chain: "Pm" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1422 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 6, 'TRANS': 177} Chain breaks: 1 Chain: "Ph" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1411 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Chain: "Pl" Number of atoms: 1402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1402 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Time building chain proxies: 4.57, per 1000 atoms: 0.23 Number of scatterers: 19981 At special positions: 0 Unit cell: (113.313, 114.372, 120.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3921 8.00 N 3404 7.00 C 12572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 872.7 milliseconds 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4806 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 47 sheets defined 51.1% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'Pb' and resid 20 through 27 removed outlier: 3.535A pdb=" N ASPPb 27 " --> pdb=" O ARGPb 23 " (cutoff:3.500A) Processing helix chain 'Pb' and resid 37 through 55 Processing helix chain 'Pb' and resid 70 through 84 Processing helix chain 'Pb' and resid 98 through 106 Processing helix chain 'Pb' and resid 133 through 159 Processing helix chain 'Pb' and resid 161 through 169 Processing helix chain 'Pb' and resid 177 through 184 Processing helix chain 'Pe' and resid 20 through 27 Processing helix chain 'Pe' and resid 37 through 55 Processing helix chain 'Pe' and resid 70 through 84 Processing helix chain 'Pe' and resid 98 through 106 Processing helix chain 'Pe' and resid 133 through 159 Processing helix chain 'Pe' and resid 161 through 170 Processing helix chain 'Pe' and resid 177 through 183 Processing helix chain 'Pa' and resid 20 through 27 removed outlier: 3.531A pdb=" N ASPPa 27 " --> pdb=" O ARGPa 23 " (cutoff:3.500A) Processing helix chain 'Pa' and resid 37 through 55 Processing helix chain 'Pa' and resid 70 through 79 removed outlier: 3.748A pdb=" N ASPPa 79 " --> pdb=" O PHEPa 75 " (cutoff:3.500A) Processing helix chain 'Pa' and resid 97 through 106 Processing helix chain 'Pa' and resid 133 through 159 Processing helix chain 'Pa' and resid 161 through 169 Processing helix chain 'Pa' and resid 177 through 184 Processing helix chain 'Pc' and resid 20 through 27 Processing helix chain 'Pc' and resid 37 through 55 Processing helix chain 'Pc' and resid 70 through 84 Processing helix chain 'Pc' and resid 98 through 106 Processing helix chain 'Pc' and resid 133 through 159 Processing helix chain 'Pc' and resid 161 through 169 Processing helix chain 'Pc' and resid 177 through 183 Processing helix chain 'Pd' and resid 20 through 27 Processing helix chain 'Pd' and resid 37 through 55 Processing helix chain 'Pd' and resid 70 through 84 Processing helix chain 'Pd' and resid 98 through 106 Processing helix chain 'Pd' and resid 133 through 159 Processing helix chain 'Pd' and resid 161 through 169 Processing helix chain 'Pd' and resid 176 through 184 Processing helix chain 'Pg' and resid 20 through 28 Processing helix chain 'Pg' and resid 37 through 55 Processing helix chain 'Pg' and resid 70 through 82 Processing helix chain 'Pg' and resid 98 through 106 Processing helix chain 'Pg' and resid 133 through 159 Processing helix chain 'Pg' and resid 161 through 169 Processing helix chain 'Pg' and resid 176 through 183 Processing helix chain 'Po' and resid 20 through 27 removed outlier: 3.737A pdb=" N ASPPo 27 " --> pdb=" O ARGPo 23 " (cutoff:3.500A) Processing helix chain 'Po' and resid 37 through 55 Processing helix chain 'Po' and resid 70 through 84 Processing helix chain 'Po' and resid 97 through 106 Processing helix chain 'Po' and resid 133 through 159 Processing helix chain 'Po' and resid 161 through 169 Processing helix chain 'Po' and resid 176 through 183 Processing helix chain 'Pf' and resid 20 through 27 Processing helix chain 'Pf' and resid 37 through 55 Processing helix chain 'Pf' and resid 70 through 84 Processing helix chain 'Pf' and resid 98 through 106 Processing helix chain 'Pf' and resid 133 through 159 Processing helix chain 'Pf' and resid 161 through 169 Processing helix chain 'Pf' and resid 177 through 184 Processing helix chain 'Pq' and resid 20 through 27 Processing helix chain 'Pq' and resid 37 through 55 Processing helix chain 'Pq' and resid 70 through 84 Processing helix chain 'Pq' and resid 97 through 106 Processing helix chain 'Pq' and resid 133 through 159 Processing helix chain 'Pq' and resid 161 through 169 Processing helix chain 'Pq' and resid 177 through 184 Processing helix chain 'Pi' and resid 20 through 27 removed outlier: 3.555A pdb=" N ASPPi 27 " --> pdb=" O ARGPi 23 " (cutoff:3.500A) Processing helix chain 'Pi' and resid 37 through 55 Processing helix chain 'Pi' and resid 70 through 84 Processing helix chain 'Pi' and resid 98 through 106 Processing helix chain 'Pi' and resid 133 through 159 Processing helix chain 'Pi' and resid 161 through 169 Processing helix chain 'Pi' and resid 177 through 183 Processing helix chain 'Pn' and resid 20 through 27 Processing helix chain 'Pn' and resid 37 through 55 Processing helix chain 'Pn' and resid 70 through 84 Processing helix chain 'Pn' and resid 97 through 106 Processing helix chain 'Pn' and resid 133 through 159 Processing helix chain 'Pn' and resid 161 through 169 Processing helix chain 'Pn' and resid 177 through 183 Processing helix chain 'Pm' and resid 20 through 27 Processing helix chain 'Pm' and resid 37 through 55 Processing helix chain 'Pm' and resid 70 through 84 Processing helix chain 'Pm' and resid 98 through 106 Processing helix chain 'Pm' and resid 133 through 159 Processing helix chain 'Pm' and resid 161 through 169 Processing helix chain 'Pm' and resid 177 through 183 Processing helix chain 'Ph' and resid 20 through 27 removed outlier: 3.723A pdb=" N ASPPh 27 " --> pdb=" O ARGPh 23 " (cutoff:3.500A) Processing helix chain 'Ph' and resid 37 through 55 Processing helix chain 'Ph' and resid 70 through 84 Processing helix chain 'Ph' and resid 98 through 106 Processing helix chain 'Ph' and resid 133 through 159 Processing helix chain 'Ph' and resid 161 through 169 Processing helix chain 'Ph' and resid 177 through 183 Processing helix chain 'Pl' and resid 20 through 27 removed outlier: 3.599A pdb=" N ASPPl 27 " --> pdb=" O ARGPl 23 " (cutoff:3.500A) Processing helix chain 'Pl' and resid 37 through 55 Processing helix chain 'Pl' and resid 70 through 84 Processing helix chain 'Pl' and resid 98 through 106 Processing helix chain 'Pl' and resid 133 through 159 Processing helix chain 'Pl' and resid 161 through 169 Processing helix chain 'Pl' and resid 177 through 183 Processing sheet with id=AA1, first strand: chain 'Pb' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'Pb' and resid 29 through 32 removed outlier: 6.611A pdb=" N ILEPb 30 " --> pdb=" O TYRPb 63 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASNPb 65 " --> pdb=" O ILEPb 30 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEUPb 32 " --> pdb=" O ASNPb 65 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N SERPb 66 " --> pdb=" O ILEPb 93 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N METPb 95 " --> pdb=" O SERPb 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Pb' and resid 29 through 32 removed outlier: 6.611A pdb=" N ILEPb 30 " --> pdb=" O TYRPb 63 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASNPb 65 " --> pdb=" O ILEPb 30 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEUPb 32 " --> pdb=" O ASNPb 65 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N SERPb 66 " --> pdb=" O ILEPb 93 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N METPb 95 " --> pdb=" O SERPb 66 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N PHEPb 113 " --> pdb=" O VALPb 88 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THRPb 90 " --> pdb=" O PHEPb 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Pb' and resid 126 through 132 Processing sheet with id=AA5, first strand: chain 'Pe' and resid 6 through 8 Processing sheet with id=AA6, first strand: chain 'Pe' and resid 29 through 32 removed outlier: 6.442A pdb=" N ILEPe 30 " --> pdb=" O TYRPe 63 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ASNPe 65 " --> pdb=" O ILEPe 30 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEUPe 32 " --> pdb=" O ASNPe 65 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N SERPe 66 " --> pdb=" O ILEPe 93 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N METPe 95 " --> pdb=" O SERPe 66 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLUPe 119 " --> pdb=" O CYSPe 92 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLYPe 94 " --> pdb=" O GLUPe 119 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N METPe 121 " --> pdb=" O GLYPe 94 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALAPe 96 " --> pdb=" O METPe 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Pe' and resid 29 through 32 removed outlier: 6.442A pdb=" N ILEPe 30 " --> pdb=" O TYRPe 63 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ASNPe 65 " --> pdb=" O ILEPe 30 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEUPe 32 " --> pdb=" O ASNPe 65 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N SERPe 66 " --> pdb=" O ILEPe 93 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N METPe 95 " --> pdb=" O SERPe 66 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N PHEPe 113 " --> pdb=" O VALPe 88 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THRPe 90 " --> pdb=" O PHEPe 113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Pe' and resid 126 through 132 Processing sheet with id=AA9, first strand: chain 'Pa' and resid 6 through 11 Processing sheet with id=AB1, first strand: chain 'Pa' and resid 29 through 32 removed outlier: 6.517A pdb=" N ILEPa 30 " --> pdb=" O TYRPa 63 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASNPa 65 " --> pdb=" O ILEPa 30 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEUPa 32 " --> pdb=" O ASNPa 65 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N SERPa 66 " --> pdb=" O ILEPa 93 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N METPa 95 " --> pdb=" O SERPa 66 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLUPa 119 " --> pdb=" O CYSPa 92 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLYPa 94 " --> pdb=" O GLUPa 119 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N METPa 121 " --> pdb=" O GLYPa 94 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALAPa 96 " --> pdb=" O METPa 121 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Pa' and resid 29 through 32 removed outlier: 6.517A pdb=" N ILEPa 30 " --> pdb=" O TYRPa 63 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ASNPa 65 " --> pdb=" O ILEPa 30 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEUPa 32 " --> pdb=" O ASNPa 65 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N SERPa 66 " --> pdb=" O ILEPa 93 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N METPa 95 " --> pdb=" O SERPa 66 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N PHEPa 113 " --> pdb=" O VALPa 88 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N THRPa 90 " --> pdb=" O PHEPa 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Pa' and resid 126 through 132 Processing sheet with id=AB4, first strand: chain 'Pc' and resid 6 through 10 Processing sheet with id=AB5, first strand: chain 'Pc' and resid 29 through 32 removed outlier: 8.578A pdb=" N SERPc 66 " --> pdb=" O ILEPc 93 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N METPc 95 " --> pdb=" O SERPc 66 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLUPc 119 " --> pdb=" O CYSPc 92 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLYPc 94 " --> pdb=" O GLUPc 119 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N METPc 121 " --> pdb=" O GLYPc 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALAPc 96 " --> pdb=" O METPc 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Pc' and resid 29 through 32 removed outlier: 8.578A pdb=" N SERPc 66 " --> pdb=" O ILEPc 93 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N METPc 95 " --> pdb=" O SERPc 66 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N PHEPc 113 " --> pdb=" O VALPc 88 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THRPc 90 " --> pdb=" O PHEPc 113 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARGPc 112 " --> pdb=" O GLUPc 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Pc' and resid 126 through 132 Processing sheet with id=AB8, first strand: chain 'Pd' and resid 6 through 10 Processing sheet with id=AB9, first strand: chain 'Pd' and resid 29 through 32 removed outlier: 6.578A pdb=" N ILEPd 30 " --> pdb=" O TYRPd 63 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ASNPd 65 " --> pdb=" O ILEPd 30 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEUPd 32 " --> pdb=" O ASNPd 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILEPd 60 " --> pdb=" O GLNPd 89 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILEPd 91 " --> pdb=" O ILEPd 60 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEUPd 62 " --> pdb=" O ILEPd 91 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILEPd 93 " --> pdb=" O LEUPd 62 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILEPd 64 " --> pdb=" O ILEPd 93 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N METPd 95 " --> pdb=" O ILEPd 64 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLUPd 119 " --> pdb=" O CYSPd 92 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLYPd 94 " --> pdb=" O GLUPd 119 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N METPd 121 " --> pdb=" O GLYPd 94 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALAPd 96 " --> pdb=" O METPd 121 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Pd' and resid 29 through 32 removed outlier: 6.578A pdb=" N ILEPd 30 " --> pdb=" O TYRPd 63 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ASNPd 65 " --> pdb=" O ILEPd 30 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEUPd 32 " --> pdb=" O ASNPd 65 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILEPd 60 " --> pdb=" O GLNPd 89 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILEPd 91 " --> pdb=" O ILEPd 60 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEUPd 62 " --> pdb=" O ILEPd 91 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILEPd 93 " --> pdb=" O LEUPd 62 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILEPd 64 " --> pdb=" O ILEPd 93 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N METPd 95 " --> pdb=" O ILEPd 64 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N PHEPd 113 " --> pdb=" O VALPd 88 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THRPd 90 " --> pdb=" O PHEPd 113 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Pd' and resid 126 through 132 Processing sheet with id=AC3, first strand: chain 'Pg' and resid 6 through 7 Processing sheet with id=AC4, first strand: chain 'Pg' and resid 29 through 32 removed outlier: 6.275A pdb=" N ILEPg 60 " --> pdb=" O GLNPg 89 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILEPg 91 " --> pdb=" O ILEPg 60 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEUPg 62 " --> pdb=" O ILEPg 91 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILEPg 93 " --> pdb=" O LEUPg 62 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILEPg 64 " --> pdb=" O ILEPg 93 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N METPg 95 " --> pdb=" O ILEPg 64 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLUPg 119 " --> pdb=" O CYSPg 92 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLYPg 94 " --> pdb=" O GLUPg 119 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N METPg 121 " --> pdb=" O GLYPg 94 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALAPg 96 " --> pdb=" O METPg 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Pg' and resid 29 through 32 removed outlier: 6.275A pdb=" N ILEPg 60 " --> pdb=" O GLNPg 89 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILEPg 91 " --> pdb=" O ILEPg 60 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEUPg 62 " --> pdb=" O ILEPg 91 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILEPg 93 " --> pdb=" O LEUPg 62 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILEPg 64 " --> pdb=" O ILEPg 93 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N METPg 95 " --> pdb=" O ILEPg 64 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N PHEPg 113 " --> pdb=" O VALPg 88 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THRPg 90 " --> pdb=" O PHEPg 113 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALAPg 114 " --> pdb=" O GLUPg 188 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Pg' and resid 126 through 132 removed outlier: 3.567A pdb=" N GLYPg 131 " --> pdb=" O GLYPh 127 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Po' and resid 29 through 32 removed outlier: 6.285A pdb=" N ILEPo 60 " --> pdb=" O GLNPo 89 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILEPo 91 " --> pdb=" O ILEPo 60 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEUPo 62 " --> pdb=" O ILEPo 91 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILEPo 93 " --> pdb=" O LEUPo 62 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILEPo 64 " --> pdb=" O ILEPo 93 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N METPo 95 " --> pdb=" O ILEPo 64 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLUPo 119 " --> pdb=" O CYSPo 92 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLYPo 94 " --> pdb=" O GLUPo 119 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N METPo 121 " --> pdb=" O GLYPo 94 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALAPo 96 " --> pdb=" O METPo 121 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Po' and resid 29 through 32 removed outlier: 6.285A pdb=" N ILEPo 60 " --> pdb=" O GLNPo 89 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILEPo 91 " --> pdb=" O ILEPo 60 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEUPo 62 " --> pdb=" O ILEPo 91 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ILEPo 93 " --> pdb=" O LEUPo 62 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILEPo 64 " --> pdb=" O ILEPo 93 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N METPo 95 " --> pdb=" O ILEPo 64 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N PHEPo 113 " --> pdb=" O VALPo 88 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N THRPo 90 " --> pdb=" O PHEPo 113 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Pf' and resid 6 through 8 Processing sheet with id=AD1, first strand: chain 'Pf' and resid 29 through 32 removed outlier: 8.738A pdb=" N SERPf 66 " --> pdb=" O ILEPf 93 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N METPf 95 " --> pdb=" O SERPf 66 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLUPf 119 " --> pdb=" O CYSPf 92 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLYPf 94 " --> pdb=" O GLUPf 119 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N METPf 121 " --> pdb=" O GLYPf 94 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALAPf 96 " --> pdb=" O METPf 121 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Pf' and resid 29 through 32 removed outlier: 8.738A pdb=" N SERPf 66 " --> pdb=" O ILEPf 93 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N METPf 95 " --> pdb=" O SERPf 66 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N PHEPf 113 " --> pdb=" O VALPf 88 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THRPf 90 " --> pdb=" O PHEPf 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALAPf 114 " --> pdb=" O GLUPf 188 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Pf' and resid 126 through 132 Processing sheet with id=AD4, first strand: chain 'Pq' and resid 29 through 32 removed outlier: 6.832A pdb=" N ILEPq 30 " --> pdb=" O TYRPq 63 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ASNPq 65 " --> pdb=" O ILEPq 30 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEUPq 32 " --> pdb=" O ASNPq 65 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILEPq 60 " --> pdb=" O GLNPq 89 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILEPq 91 " --> pdb=" O ILEPq 60 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEUPq 62 " --> pdb=" O ILEPq 91 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILEPq 93 " --> pdb=" O LEUPq 62 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILEPq 64 " --> pdb=" O ILEPq 93 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N METPq 95 " --> pdb=" O ILEPq 64 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLUPq 119 " --> pdb=" O CYSPq 92 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLYPq 94 " --> pdb=" O GLUPq 119 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N METPq 121 " --> pdb=" O GLYPq 94 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALAPq 96 " --> pdb=" O METPq 121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Pq' and resid 29 through 32 removed outlier: 6.832A pdb=" N ILEPq 30 " --> pdb=" O TYRPq 63 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ASNPq 65 " --> pdb=" O ILEPq 30 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEUPq 32 " --> pdb=" O ASNPq 65 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILEPq 60 " --> pdb=" O GLNPq 89 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILEPq 91 " --> pdb=" O ILEPq 60 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEUPq 62 " --> pdb=" O ILEPq 91 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILEPq 93 " --> pdb=" O LEUPq 62 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILEPq 64 " --> pdb=" O ILEPq 93 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N METPq 95 " --> pdb=" O ILEPq 64 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N PHEPq 113 " --> pdb=" O VALPq 88 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THRPq 90 " --> pdb=" O PHEPq 113 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Pi' and resid 6 through 7 Processing sheet with id=AD7, first strand: chain 'Pi' and resid 29 through 32 removed outlier: 6.648A pdb=" N ILEPi 30 " --> pdb=" O TYRPi 63 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASNPi 65 " --> pdb=" O ILEPi 30 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEUPi 32 " --> pdb=" O ASNPi 65 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N SERPi 66 " --> pdb=" O ILEPi 93 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N METPi 95 " --> pdb=" O SERPi 66 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLUPi 119 " --> pdb=" O CYSPi 92 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLYPi 94 " --> pdb=" O GLUPi 119 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N METPi 121 " --> pdb=" O GLYPi 94 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALAPi 96 " --> pdb=" O METPi 121 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Pi' and resid 29 through 32 removed outlier: 6.648A pdb=" N ILEPi 30 " --> pdb=" O TYRPi 63 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASNPi 65 " --> pdb=" O ILEPi 30 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEUPi 32 " --> pdb=" O ASNPi 65 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N SERPi 66 " --> pdb=" O ILEPi 93 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N METPi 95 " --> pdb=" O SERPi 66 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHEPi 113 " --> pdb=" O VALPi 88 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THRPi 90 " --> pdb=" O PHEPi 113 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALAPi 114 " --> pdb=" O GLUPi 188 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Pn' and resid 6 through 7 Processing sheet with id=AE1, first strand: chain 'Pn' and resid 29 through 32 removed outlier: 8.950A pdb=" N SERPn 66 " --> pdb=" O ILEPn 93 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N METPn 95 " --> pdb=" O SERPn 66 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLUPn 119 " --> pdb=" O CYSPn 92 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLYPn 94 " --> pdb=" O GLUPn 119 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N METPn 121 " --> pdb=" O GLYPn 94 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALAPn 96 " --> pdb=" O METPn 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Pn' and resid 29 through 32 removed outlier: 8.950A pdb=" N SERPn 66 " --> pdb=" O ILEPn 93 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N METPn 95 " --> pdb=" O SERPn 66 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHEPn 113 " --> pdb=" O VALPn 88 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THRPn 90 " --> pdb=" O PHEPn 113 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Pm' and resid 6 through 7 Processing sheet with id=AE4, first strand: chain 'Pm' and resid 29 through 32 removed outlier: 6.195A pdb=" N ILEPm 60 " --> pdb=" O GLNPm 89 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILEPm 91 " --> pdb=" O ILEPm 60 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEUPm 62 " --> pdb=" O ILEPm 91 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILEPm 93 " --> pdb=" O LEUPm 62 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILEPm 64 " --> pdb=" O ILEPm 93 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N METPm 95 " --> pdb=" O ILEPm 64 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLUPm 119 " --> pdb=" O CYSPm 92 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLYPm 94 " --> pdb=" O GLUPm 119 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N METPm 121 " --> pdb=" O GLYPm 94 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALAPm 96 " --> pdb=" O METPm 121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Pm' and resid 29 through 32 removed outlier: 6.195A pdb=" N ILEPm 60 " --> pdb=" O GLNPm 89 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILEPm 91 " --> pdb=" O ILEPm 60 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEUPm 62 " --> pdb=" O ILEPm 91 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILEPm 93 " --> pdb=" O LEUPm 62 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILEPm 64 " --> pdb=" O ILEPm 93 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N METPm 95 " --> pdb=" O ILEPm 64 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N PHEPm 113 " --> pdb=" O VALPm 88 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THRPm 90 " --> pdb=" O PHEPm 113 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Ph' and resid 6 through 7 Processing sheet with id=AE7, first strand: chain 'Ph' and resid 29 through 32 removed outlier: 8.581A pdb=" N SERPh 66 " --> pdb=" O ILEPh 93 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N METPh 95 " --> pdb=" O SERPh 66 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLUPh 119 " --> pdb=" O CYSPh 92 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLYPh 94 " --> pdb=" O GLUPh 119 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N METPh 121 " --> pdb=" O GLYPh 94 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALAPh 96 " --> pdb=" O METPh 121 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Ph' and resid 29 through 32 removed outlier: 8.581A pdb=" N SERPh 66 " --> pdb=" O ILEPh 93 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N METPh 95 " --> pdb=" O SERPh 66 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N PHEPh 113 " --> pdb=" O VALPh 88 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THRPh 90 " --> pdb=" O PHEPh 113 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Pl' and resid 6 through 7 Processing sheet with id=AF1, first strand: chain 'Pl' and resid 29 through 32 removed outlier: 8.671A pdb=" N SERPl 66 " --> pdb=" O ILEPl 93 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N METPl 95 " --> pdb=" O SERPl 66 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLUPl 119 " --> pdb=" O CYSPl 92 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLYPl 94 " --> pdb=" O GLUPl 119 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N METPl 121 " --> pdb=" O GLYPl 94 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALAPl 96 " --> pdb=" O METPl 121 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Pl' and resid 29 through 32 removed outlier: 8.671A pdb=" N SERPl 66 " --> pdb=" O ILEPl 93 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N METPl 95 " --> pdb=" O SERPl 66 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N PHEPl 113 " --> pdb=" O VALPl 88 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N THRPl 90 " --> pdb=" O PHEPl 113 " (cutoff:3.500A) 1249 hydrogen bonds defined for protein. 3639 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: 3.88 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6774 1.34 - 1.46: 2247 1.46 - 1.57: 11061 1.57 - 1.69: 0 1.69 - 1.81: 154 Bond restraints: 20236 Sorted by residual: bond pdb=" CA TYRPa 78 " pdb=" C TYRPa 78 " ideal model delta sigma weight residual 1.523 1.506 0.017 1.30e-02 5.92e+03 1.69e+00 bond pdb=" CG1 ILEPg 165 " pdb=" CD1 ILEPg 165 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.29e+00 bond pdb=" CG1 ILEPe 165 " pdb=" CD1 ILEPe 165 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.25e+00 bond pdb=" N ASPPa 79 " pdb=" CA ASPPa 79 " ideal model delta sigma weight residual 1.458 1.445 0.013 1.27e-02 6.20e+03 1.10e+00 bond pdb=" CG1 ILEPl 165 " pdb=" CD1 ILEPl 165 " ideal model delta sigma weight residual 1.513 1.473 0.040 3.90e-02 6.57e+02 1.06e+00 ... (remaining 20231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 26667 1.87 - 3.74: 574 3.74 - 5.61: 55 5.61 - 7.48: 16 7.48 - 9.34: 3 Bond angle restraints: 27315 Sorted by residual: angle pdb=" N GLYPe 131 " pdb=" CA GLYPe 131 " pdb=" C GLYPe 131 " ideal model delta sigma weight residual 110.83 119.77 -8.94 1.91e+00 2.74e-01 2.19e+01 angle pdb=" C GLNPe 130 " pdb=" N GLYPe 131 " pdb=" CA GLYPe 131 " ideal model delta sigma weight residual 121.22 111.88 9.34 2.07e+00 2.33e-01 2.04e+01 angle pdb=" N GLNPe 132 " pdb=" CA GLNPe 132 " pdb=" C GLNPe 132 " ideal model delta sigma weight residual 110.17 102.93 7.24 1.61e+00 3.86e-01 2.02e+01 angle pdb=" N GLYPc 14 " pdb=" CA GLYPc 14 " pdb=" C GLYPc 14 " ideal model delta sigma weight residual 111.14 118.88 -7.74 1.80e+00 3.09e-01 1.85e+01 angle pdb=" N GLNPb 132 " pdb=" CA GLNPb 132 " pdb=" C GLNPb 132 " ideal model delta sigma weight residual 110.32 104.12 6.20 1.59e+00 3.96e-01 1.52e+01 ... (remaining 27310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 11328 17.56 - 35.11: 828 35.11 - 52.67: 176 52.67 - 70.22: 81 70.22 - 87.78: 29 Dihedral angle restraints: 12442 sinusoidal: 4986 harmonic: 7456 Sorted by residual: dihedral pdb=" CA GLYPe 131 " pdb=" C GLYPe 131 " pdb=" N GLNPe 132 " pdb=" CA GLNPe 132 " ideal model delta harmonic sigma weight residual 180.00 148.25 31.75 0 5.00e+00 4.00e-02 4.03e+01 dihedral pdb=" CA ARGPc 13 " pdb=" C ARGPc 13 " pdb=" N GLYPc 14 " pdb=" CA GLYPc 14 " ideal model delta harmonic sigma weight residual 180.00 -148.45 -31.55 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA GLNPe 130 " pdb=" C GLNPe 130 " pdb=" N GLYPe 131 " pdb=" CA GLYPe 131 " ideal model delta harmonic sigma weight residual -180.00 -148.78 -31.22 0 5.00e+00 4.00e-02 3.90e+01 ... (remaining 12439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2591 0.059 - 0.118: 518 0.118 - 0.178: 71 0.178 - 0.237: 0 0.237 - 0.296: 1 Chirality restraints: 3181 Sorted by residual: chirality pdb=" CB ILEPa 84 " pdb=" CA ILEPa 84 " pdb=" CG1 ILEPa 84 " pdb=" CG2 ILEPa 84 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CB ILEPa 81 " pdb=" CA ILEPa 81 " pdb=" CG1 ILEPa 81 " pdb=" CG2 ILEPa 81 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA ILEPq 60 " pdb=" N ILEPq 60 " pdb=" C ILEPq 60 " pdb=" CB ILEPq 60 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.17e-01 ... (remaining 3178 not shown) Planarity restraints: 3561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGPc 16 " -0.282 9.50e-02 1.11e+02 1.27e-01 1.17e+01 pdb=" NE ARGPc 16 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARGPc 16 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARGPc 16 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARGPc 16 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGPf 28 " 0.262 9.50e-02 1.11e+02 1.18e-01 9.33e+00 pdb=" NE ARGPf 28 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARGPf 28 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARGPf 28 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARGPf 28 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARGPb 28 " 0.231 9.50e-02 1.11e+02 1.04e-01 7.45e+00 pdb=" NE ARGPb 28 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARGPb 28 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARGPb 28 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARGPb 28 " 0.003 2.00e-02 2.50e+03 ... (remaining 3558 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2709 2.76 - 3.30: 19917 3.30 - 3.83: 34234 3.83 - 4.37: 41492 4.37 - 4.90: 71979 Nonbonded interactions: 170331 Sorted by model distance: nonbonded pdb=" O ALAPq 97 " pdb=" N GLYPq 100 " model vdw 2.227 3.120 nonbonded pdb=" O ASPPa 79 " pdb=" OG1 THRPa 80 " model vdw 2.256 3.040 nonbonded pdb=" O ALAPa 97 " pdb=" N GLYPa 100 " model vdw 2.258 3.120 nonbonded pdb=" O ALAPo 97 " pdb=" N GLYPo 100 " model vdw 2.268 3.120 nonbonded pdb=" O ALAPn 97 " pdb=" N GLYPn 100 " model vdw 2.313 3.120 ... (remaining 170326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'Pa' and (resid 5 through 8 or resid 19 through 166 or (resid 167 and (na \ me N or name CA or name C or name O or name CB )) or resid 168 through 192)) selection = (chain 'Pb' and (resid 5 through 8 or resid 19 through 166 or (resid 167 and (na \ me N or name CA or name C or name O or name CB )) or resid 168 through 192)) selection = (chain 'Pc' and (resid 5 through 8 or resid 19 through 166 or (resid 167 and (na \ me N or name CA or name C or name O or name CB )) or resid 168 through 192)) selection = (chain 'Pd' and (resid 5 through 8 or resid 19 through 166 or (resid 167 and (na \ me N or name CA or name C or name O or name CB )) or resid 168 through 192)) selection = (chain 'Pe' and (resid 5 through 8 or resid 19 through 192)) selection = (chain 'Pf' and (resid 5 through 8 or resid 19 through 166 or (resid 167 and (na \ me N or name CA or name C or name O or name CB )) or resid 168 through 192)) selection = (chain 'Pg' and (resid 5 through 8 or resid 19 through 166 or (resid 167 and (na \ me N or name CA or name C or name O or name CB )) or resid 168 through 192)) selection = (chain 'Ph' and (resid 5 through 8 or resid 19 through 166 or (resid 167 and (na \ me N or name CA or name C or name O or name CB )) or resid 168 through 192)) selection = (chain 'Pi' and (resid 5 through 8 or resid 19 through 166 or (resid 167 and (na \ me N or name CA or name C or name O or name CB )) or resid 168 through 192)) selection = (chain 'Pl' and (resid 5 through 8 or resid 19 through 166 or (resid 167 and (na \ me N or name CA or name C or name O or name CB )) or resid 168 through 192)) selection = (chain 'Pm' and (resid 5 through 8 or resid 19 through 166 or (resid 167 and (na \ me N or name CA or name C or name O or name CB )) or resid 168 through 192)) selection = (chain 'Pn' and (resid 5 through 8 or resid 19 through 166 or (resid 167 and (na \ me N or name CA or name C or name O or name CB )) or resid 168 through 192)) selection = (chain 'Po' and (resid 5 through 8 or resid 19 through 166 or (resid 167 and (na \ me N or name CA or name C or name O or name CB )) or resid 168 through 192)) selection = (chain 'Pq' and (resid 5 through 8 or resid 19 through 166 or (resid 167 and (na \ me N or name CA or name C or name O or name CB )) or resid 168 through 192)) } 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: 4.380 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.110 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 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 : 0.004 0.044 20236 Z= 0.158 Angle : 0.693 9.345 27315 Z= 0.416 Chirality : 0.048 0.296 3181 Planarity : 0.009 0.127 3561 Dihedral : 14.770 87.778 7636 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.55 % Favored : 97.05 % Rotamer: Outliers : 1.26 % Allowed : 4.88 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.14), residues: 2545 helix: -0.58 (0.12), residues: 1373 sheet: 0.47 (0.31), residues: 221 loop : -0.83 (0.18), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.004 ARGPc 16 TYR 0.024 0.005 TYRPa 78 PHE 0.014 0.002 PHEPa 102 HIS 0.006 0.002 HISPo 123 Details of bonding type rmsd covalent geometry : bond 0.00351 (20236) covalent geometry : angle 0.69268 (27315) hydrogen bonds : bond 0.13864 ( 1164) hydrogen bonds : angle 6.51154 ( 3639) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 373 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: Pb 132 GLN cc_start: 0.7802 (mt0) cc_final: 0.7572 (mt0) REVERT: Pa 31 MET cc_start: 0.9121 (mmt) cc_final: 0.8724 (mmt) REVERT: Pc 39 ASN cc_start: 0.8198 (m-40) cc_final: 0.7886 (m110) REVERT: Po 156 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8696 (mt-10) REVERT: Po 172 ASP cc_start: 0.8073 (m-30) cc_final: 0.7732 (m-30) REVERT: Po 178 GLU cc_start: 0.9078 (mp0) cc_final: 0.8877 (mp0) REVERT: Pf 87 ASP cc_start: 0.8544 (m-30) cc_final: 0.8325 (m-30) REVERT: Pq 23 ARG cc_start: 0.6297 (mmt-90) cc_final: 0.5240 (tpt90) REVERT: Pq 35 GLN cc_start: 0.8645 (tt0) cc_final: 0.7851 (pp30) REVERT: Pq 163 GLU cc_start: 0.8573 (mp0) cc_final: 0.8337 (mp0) REVERT: Pi 171 ARG cc_start: 0.9157 (mmt180) cc_final: 0.8908 (mmt180) REVERT: Pn 121 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8764 (ttt) REVERT: Pn 160 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7836 (mp10) outliers start: 27 outliers final: 10 residues processed: 392 average time/residue: 0.8270 time to fit residues: 355.6666 Evaluate side-chains 281 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 269 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Pe residue 31 MET Chi-restraints excluded: chain Pe residue 40 VAL Chi-restraints excluded: chain Pg residue 24 LEU Chi-restraints excluded: chain Pg residue 32 LEU Chi-restraints excluded: chain Pg residue 40 VAL Chi-restraints excluded: chain Pg residue 117 ASN Chi-restraints excluded: chain Pg residue 121 MET Chi-restraints excluded: chain Pi residue 161 SER Chi-restraints excluded: chain Pn residue 27 ASP Chi-restraints excluded: chain Pn residue 121 MET Chi-restraints excluded: chain Pn residue 160 GLN Chi-restraints excluded: chain Pm residue 40 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 0.1980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Pb 54 GLN Pb 130 GLN Pb 166 GLN Pe 47 GLN Pe 117 ASN Pa 39 ASN Pa 173 ASN Pc 42 ASN Pc 123 HIS Pc 166 GLN Pd 117 ASN Pd 123 HIS Pd 173 ASN Pg 39 ASN Pg 166 GLN Pg 173 ASN Pf 52 GLN Pq 47 GLN Pi 123 HIS Pi 173 ASN Pn 39 ASN Ph 117 ASN Ph 124 GLN Pl 47 GLN Pl 117 ASN ** Pl 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.053110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.047861 restraints weight = 46521.797| |-----------------------------------------------------------------------------| r_work (start): 0.2565 rms_B_bonded: 1.52 r_work: 0.2484 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2397 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20236 Z= 0.165 Angle : 0.601 6.074 27315 Z= 0.324 Chirality : 0.046 0.151 3181 Planarity : 0.004 0.047 3561 Dihedral : 5.766 58.412 2785 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.14 % Allowed : 11.30 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.16), residues: 2545 helix: 1.20 (0.13), residues: 1386 sheet: 0.07 (0.30), residues: 231 loop : -0.55 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGPb 16 TYR 0.016 0.002 TYRPf 18 PHE 0.013 0.002 PHEPg 50 HIS 0.005 0.001 HISPi 142 Details of bonding type rmsd covalent geometry : bond 0.00395 (20236) covalent geometry : angle 0.60059 (27315) hydrogen bonds : bond 0.04368 ( 1164) hydrogen bonds : angle 4.27936 ( 3639) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 281 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: Pa 31 MET cc_start: 0.9297 (mmt) cc_final: 0.9010 (mmt) REVERT: Pc 27 ASP cc_start: 0.8570 (m-30) cc_final: 0.8240 (m-30) REVERT: Pd 173 ASN cc_start: 0.8601 (t0) cc_final: 0.8340 (t160) REVERT: Pg 27 ASP cc_start: 0.7511 (m-30) cc_final: 0.7181 (m-30) REVERT: Po 135 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8663 (mt-10) REVERT: Pq 23 ARG cc_start: 0.6419 (mmt-90) cc_final: 0.5007 (tpt90) REVERT: Pq 35 GLN cc_start: 0.8829 (tt0) cc_final: 0.7333 (pp30) REVERT: Pq 163 GLU cc_start: 0.8805 (mp0) cc_final: 0.8528 (mp0) REVERT: Pn 27 ASP cc_start: 0.9302 (OUTLIER) cc_final: 0.8810 (m-30) REVERT: Pn 160 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.7401 (mp10) REVERT: Pm 23 ARG cc_start: 0.8829 (tpt90) cc_final: 0.8543 (mmm160) REVERT: Pm 42 ASN cc_start: 0.8695 (t0) cc_final: 0.8450 (t0) REVERT: Pm 62 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8710 (tt) REVERT: Pm 160 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8285 (mp10) REVERT: Pl 109 LYS cc_start: 0.9405 (mtmm) cc_final: 0.9194 (mppt) REVERT: Pl 119 GLU cc_start: 0.8744 (pt0) cc_final: 0.8448 (pt0) outliers start: 46 outliers final: 18 residues processed: 305 average time/residue: 0.8681 time to fit residues: 289.8458 Evaluate side-chains 272 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 250 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Pb residue 162 ILE Chi-restraints excluded: chain Pe residue 40 VAL Chi-restraints excluded: chain Pa residue 7 VAL Chi-restraints excluded: chain Pa residue 121 MET Chi-restraints excluded: chain Pa residue 182 GLU Chi-restraints excluded: chain Pc residue 8 ILE Chi-restraints excluded: chain Pc residue 31 MET Chi-restraints excluded: chain Pd residue 191 VAL Chi-restraints excluded: chain Pg residue 7 VAL Chi-restraints excluded: chain Pg residue 24 LEU Chi-restraints excluded: chain Po residue 162 ILE Chi-restraints excluded: chain Pf residue 190 MET Chi-restraints excluded: chain Pq residue 119 GLU Chi-restraints excluded: chain Pi residue 19 ASP Chi-restraints excluded: chain Pn residue 27 ASP Chi-restraints excluded: chain Pn residue 119 GLU Chi-restraints excluded: chain Pn residue 160 GLN Chi-restraints excluded: chain Pm residue 19 ASP Chi-restraints excluded: chain Pm residue 62 LEU Chi-restraints excluded: chain Pm residue 160 GLN Chi-restraints excluded: chain Pm residue 191 VAL Chi-restraints excluded: chain Pl residue 163 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 117 optimal weight: 0.7980 chunk 176 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 188 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Pb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Pb 117 ASN Pa 47 GLN Pa 173 ASN Pl 39 ASN Pl 42 ASN ** Pl 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.051422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.046247 restraints weight = 47418.721| |-----------------------------------------------------------------------------| r_work (start): 0.2523 rms_B_bonded: 1.51 r_work: 0.2441 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2355 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20236 Z= 0.177 Angle : 0.587 5.902 27315 Z= 0.315 Chirality : 0.045 0.152 3181 Planarity : 0.005 0.049 3561 Dihedral : 5.331 59.476 2769 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.02 % Allowed : 12.27 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 2545 helix: 1.53 (0.14), residues: 1385 sheet: -0.04 (0.30), residues: 255 loop : -0.65 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGPb 16 TYR 0.015 0.002 TYRPl 18 PHE 0.011 0.001 PHEPg 50 HIS 0.005 0.001 HISPf 142 Details of bonding type rmsd covalent geometry : bond 0.00431 (20236) covalent geometry : angle 0.58705 (27315) hydrogen bonds : bond 0.04441 ( 1164) hydrogen bonds : angle 4.15451 ( 3639) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 261 time to evaluate : 0.816 Fit side-chains REVERT: Pa 31 MET cc_start: 0.9346 (mmt) cc_final: 0.9115 (mmt) REVERT: Pc 27 ASP cc_start: 0.8534 (m-30) cc_final: 0.8222 (m-30) REVERT: Pd 18 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: Pd 95 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8037 (tpp) REVERT: Pd 173 ASN cc_start: 0.8592 (t0) cc_final: 0.8272 (t160) REVERT: Pg 27 ASP cc_start: 0.8216 (m-30) cc_final: 0.7995 (m-30) REVERT: Po 156 GLU cc_start: 0.9264 (mt-10) cc_final: 0.9048 (mt-10) REVERT: Po 178 GLU cc_start: 0.9111 (mp0) cc_final: 0.8897 (mp0) REVERT: Pf 26 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8749 (tttp) REVERT: Pq 9 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7160 (mt-10) REVERT: Pq 23 ARG cc_start: 0.6470 (mmt-90) cc_final: 0.5008 (tpt90) REVERT: Pq 35 GLN cc_start: 0.8899 (tt0) cc_final: 0.7447 (pp30) REVERT: Pq 163 GLU cc_start: 0.8871 (mp0) cc_final: 0.8527 (mp0) REVERT: Pi 23 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7868 (tpt-90) REVERT: Pn 27 ASP cc_start: 0.9308 (OUTLIER) cc_final: 0.8841 (m-30) REVERT: Pn 160 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.7314 (mp10) REVERT: Pm 62 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8836 (tt) REVERT: Pm 160 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.8254 (mp10) REVERT: Ph 121 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.8718 (ttp) REVERT: Pl 109 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9158 (mppt) outliers start: 65 outliers final: 29 residues processed: 291 average time/residue: 0.8317 time to fit residues: 264.4519 Evaluate side-chains 281 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 241 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Pb residue 18 TYR Chi-restraints excluded: chain Pb residue 26 LYS Chi-restraints excluded: chain Pb residue 154 LEU Chi-restraints excluded: chain Pb residue 162 ILE Chi-restraints excluded: chain Pb residue 191 VAL Chi-restraints excluded: chain Pe residue 40 VAL Chi-restraints excluded: chain Pe residue 119 GLU Chi-restraints excluded: chain Pe residue 185 LEU Chi-restraints excluded: chain Pa residue 121 MET Chi-restraints excluded: chain Pc residue 8 ILE Chi-restraints excluded: chain Pc residue 31 MET Chi-restraints excluded: chain Pc residue 188 GLU Chi-restraints excluded: chain Pd residue 16 ARG Chi-restraints excluded: chain Pd residue 18 TYR Chi-restraints excluded: chain Pd residue 95 MET Chi-restraints excluded: chain Pd residue 191 VAL Chi-restraints excluded: chain Pg residue 24 LEU Chi-restraints excluded: chain Pg residue 121 MET Chi-restraints excluded: chain Po residue 162 ILE Chi-restraints excluded: chain Pf residue 26 LYS Chi-restraints excluded: chain Pq residue 9 GLU Chi-restraints excluded: chain Pq residue 119 GLU Chi-restraints excluded: chain Pq residue 190 MET Chi-restraints excluded: chain Pi residue 23 ARG Chi-restraints excluded: chain Pi residue 191 VAL Chi-restraints excluded: chain Pn residue 27 ASP Chi-restraints excluded: chain Pn residue 32 LEU Chi-restraints excluded: chain Pn residue 35 GLN Chi-restraints excluded: chain Pn residue 119 GLU Chi-restraints excluded: chain Pn residue 160 GLN Chi-restraints excluded: chain Pm residue 62 LEU Chi-restraints excluded: chain Pm residue 98 SER Chi-restraints excluded: chain Pm residue 160 GLN Chi-restraints excluded: chain Pm residue 190 MET Chi-restraints excluded: chain Pm residue 191 VAL Chi-restraints excluded: chain Ph residue 121 MET Chi-restraints excluded: chain Ph residue 126 LEU Chi-restraints excluded: chain Pl residue 109 LYS Chi-restraints excluded: chain Pl residue 163 GLU Chi-restraints excluded: chain Pl residue 190 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 chunk 197 optimal weight: 0.4980 chunk 244 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Pb 39 ASN ** Pb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Pe 42 ASN Pl 39 ASN Pl 52 GLN Pl 123 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.051979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.046821 restraints weight = 47153.965| |-----------------------------------------------------------------------------| r_work (start): 0.2538 rms_B_bonded: 1.52 r_work: 0.2457 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2371 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20236 Z= 0.154 Angle : 0.551 5.352 27315 Z= 0.294 Chirality : 0.044 0.150 3181 Planarity : 0.004 0.039 3561 Dihedral : 5.164 59.336 2769 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.60 % Allowed : 13.76 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.16), residues: 2545 helix: 1.75 (0.14), residues: 1387 sheet: -0.12 (0.31), residues: 232 loop : -0.70 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGPc 23 TYR 0.016 0.001 TYRPl 18 PHE 0.010 0.001 PHEPg 50 HIS 0.004 0.001 HISPf 142 Details of bonding type rmsd covalent geometry : bond 0.00370 (20236) covalent geometry : angle 0.55093 (27315) hydrogen bonds : bond 0.04049 ( 1164) hydrogen bonds : angle 3.94511 ( 3639) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 253 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: Pb 55 ASP cc_start: 0.8360 (t0) cc_final: 0.8074 (t0) REVERT: Pa 31 MET cc_start: 0.9350 (mmt) cc_final: 0.9118 (mmt) REVERT: Pc 27 ASP cc_start: 0.8471 (m-30) cc_final: 0.7859 (m-30) REVERT: Pd 95 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8081 (tpp) REVERT: Pd 173 ASN cc_start: 0.8591 (t0) cc_final: 0.8312 (t160) REVERT: Pf 18 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: Pf 26 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8664 (tttp) REVERT: Pq 23 ARG cc_start: 0.6601 (mmt-90) cc_final: 0.5184 (tpt90) REVERT: Pq 35 GLN cc_start: 0.8922 (tt0) cc_final: 0.7503 (pp30) REVERT: Pq 163 GLU cc_start: 0.8881 (mp0) cc_final: 0.8473 (mp0) REVERT: Pi 23 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7860 (tpt-90) REVERT: Pi 95 MET cc_start: 0.9048 (tpt) cc_final: 0.8538 (tpt) REVERT: Pi 121 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.8733 (ttm) REVERT: Pn 27 ASP cc_start: 0.9265 (OUTLIER) cc_final: 0.8747 (m-30) REVERT: Pn 160 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.7280 (mp10) REVERT: Pm 62 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8852 (tt) REVERT: Pm 160 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8190 (mp10) REVERT: Pl 109 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9157 (mppt) outliers start: 56 outliers final: 28 residues processed: 277 average time/residue: 0.8716 time to fit residues: 263.5500 Evaluate side-chains 273 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Pb residue 18 TYR Chi-restraints excluded: chain Pb residue 26 LYS Chi-restraints excluded: chain Pb residue 162 ILE Chi-restraints excluded: chain Pb residue 191 VAL Chi-restraints excluded: chain Pe residue 40 VAL Chi-restraints excluded: chain Pe residue 119 GLU Chi-restraints excluded: chain Pe residue 162 ILE Chi-restraints excluded: chain Pe residue 185 LEU Chi-restraints excluded: chain Pa residue 7 VAL Chi-restraints excluded: chain Pa residue 121 MET Chi-restraints excluded: chain Pa residue 182 GLU Chi-restraints excluded: chain Pc residue 31 MET Chi-restraints excluded: chain Pc residue 191 VAL Chi-restraints excluded: chain Pd residue 95 MET Chi-restraints excluded: chain Pd residue 191 VAL Chi-restraints excluded: chain Pg residue 24 LEU Chi-restraints excluded: chain Po residue 162 ILE Chi-restraints excluded: chain Pf residue 18 TYR Chi-restraints excluded: chain Pf residue 26 LYS Chi-restraints excluded: chain Pq residue 119 GLU Chi-restraints excluded: chain Pq residue 190 MET Chi-restraints excluded: chain Pi residue 23 ARG Chi-restraints excluded: chain Pi residue 121 MET Chi-restraints excluded: chain Pi residue 191 VAL Chi-restraints excluded: chain Pn residue 27 ASP Chi-restraints excluded: chain Pn residue 32 LEU Chi-restraints excluded: chain Pn residue 35 GLN Chi-restraints excluded: chain Pn residue 119 GLU Chi-restraints excluded: chain Pn residue 160 GLN Chi-restraints excluded: chain Pm residue 19 ASP Chi-restraints excluded: chain Pm residue 62 LEU Chi-restraints excluded: chain Pm residue 98 SER Chi-restraints excluded: chain Pm residue 160 GLN Chi-restraints excluded: chain Pm residue 190 MET Chi-restraints excluded: chain Pm residue 191 VAL Chi-restraints excluded: chain Ph residue 126 LEU Chi-restraints excluded: chain Pl residue 109 LYS Chi-restraints excluded: chain Pl residue 163 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 169 optimal weight: 2.9990 chunk 226 optimal weight: 4.9990 chunk 230 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 245 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Pb 39 ASN ** Pb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Pe 42 ASN Pc 117 ASN ** Pd 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Pg 117 ASN Pl 39 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.051410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.046267 restraints weight = 47077.301| |-----------------------------------------------------------------------------| r_work (start): 0.2524 rms_B_bonded: 1.51 r_work: 0.2443 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2358 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20236 Z= 0.168 Angle : 0.564 6.193 27315 Z= 0.301 Chirality : 0.044 0.150 3181 Planarity : 0.004 0.041 3561 Dihedral : 5.158 58.647 2769 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.12 % Favored : 97.84 % Rotamer: Outliers : 3.16 % Allowed : 13.81 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.16), residues: 2545 helix: 1.77 (0.14), residues: 1386 sheet: -0.18 (0.32), residues: 221 loop : -0.77 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGPc 23 TYR 0.016 0.001 TYRPm 18 PHE 0.010 0.001 PHEPg 50 HIS 0.004 0.001 HISPf 142 Details of bonding type rmsd covalent geometry : bond 0.00406 (20236) covalent geometry : angle 0.56392 (27315) hydrogen bonds : bond 0.04144 ( 1164) hydrogen bonds : angle 3.94300 ( 3639) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 244 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: Pb 55 ASP cc_start: 0.8370 (t0) cc_final: 0.8082 (t0) REVERT: Pa 31 MET cc_start: 0.9341 (mmt) cc_final: 0.9126 (mmt) REVERT: Pc 27 ASP cc_start: 0.8490 (m-30) cc_final: 0.7919 (m-30) REVERT: Pc 35 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: Pd 18 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7168 (m-80) REVERT: Pd 95 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8071 (tpp) REVERT: Pd 173 ASN cc_start: 0.8587 (t0) cc_final: 0.8287 (t160) REVERT: Pf 18 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.8253 (m-80) REVERT: Pf 26 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8649 (tttp) REVERT: Pq 9 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7164 (mt-10) REVERT: Pq 23 ARG cc_start: 0.6494 (mmt-90) cc_final: 0.5096 (tpt90) REVERT: Pq 35 GLN cc_start: 0.8926 (tt0) cc_final: 0.7512 (pp30) REVERT: Pq 99 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7880 (mmp) REVERT: Pi 23 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7880 (tpt-90) REVERT: Pi 95 MET cc_start: 0.9039 (tpt) cc_final: 0.8554 (tpt) REVERT: Pi 121 MET cc_start: 0.9355 (OUTLIER) cc_final: 0.8746 (ttm) REVERT: Pn 27 ASP cc_start: 0.9274 (OUTLIER) cc_final: 0.8786 (m-30) REVERT: Pn 160 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: Pm 62 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8857 (tt) REVERT: Pm 160 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.8239 (mp10) REVERT: Pl 109 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.9163 (mppt) outliers start: 68 outliers final: 38 residues processed: 278 average time/residue: 0.8498 time to fit residues: 258.6700 Evaluate side-chains 288 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 236 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Pb residue 18 TYR Chi-restraints excluded: chain Pb residue 26 LYS Chi-restraints excluded: chain Pb residue 121 MET Chi-restraints excluded: chain Pb residue 154 LEU Chi-restraints excluded: chain Pb residue 162 ILE Chi-restraints excluded: chain Pb residue 191 VAL Chi-restraints excluded: chain Pe residue 40 VAL Chi-restraints excluded: chain Pe residue 119 GLU Chi-restraints excluded: chain Pe residue 162 ILE Chi-restraints excluded: chain Pe residue 185 LEU Chi-restraints excluded: chain Pa residue 7 VAL Chi-restraints excluded: chain Pa residue 57 GLU Chi-restraints excluded: chain Pa residue 109 LYS Chi-restraints excluded: chain Pa residue 121 MET Chi-restraints excluded: chain Pa residue 182 GLU Chi-restraints excluded: chain Pc residue 31 MET Chi-restraints excluded: chain Pc residue 35 GLN Chi-restraints excluded: chain Pc residue 191 VAL Chi-restraints excluded: chain Pd residue 18 TYR Chi-restraints excluded: chain Pd residue 95 MET Chi-restraints excluded: chain Pd residue 191 VAL Chi-restraints excluded: chain Pg residue 7 VAL Chi-restraints excluded: chain Pg residue 24 LEU Chi-restraints excluded: chain Pg residue 121 MET Chi-restraints excluded: chain Po residue 162 ILE Chi-restraints excluded: chain Pf residue 18 TYR Chi-restraints excluded: chain Pf residue 26 LYS Chi-restraints excluded: chain Pq residue 9 GLU Chi-restraints excluded: chain Pq residue 99 MET Chi-restraints excluded: chain Pq residue 119 GLU Chi-restraints excluded: chain Pq residue 190 MET Chi-restraints excluded: chain Pi residue 19 ASP Chi-restraints excluded: chain Pi residue 23 ARG Chi-restraints excluded: chain Pi residue 93 ILE Chi-restraints excluded: chain Pi residue 121 MET Chi-restraints excluded: chain Pi residue 191 VAL Chi-restraints excluded: chain Pn residue 27 ASP Chi-restraints excluded: chain Pn residue 32 LEU Chi-restraints excluded: chain Pn residue 35 GLN Chi-restraints excluded: chain Pn residue 119 GLU Chi-restraints excluded: chain Pn residue 160 GLN Chi-restraints excluded: chain Pm residue 62 LEU Chi-restraints excluded: chain Pm residue 72 THR Chi-restraints excluded: chain Pm residue 98 SER Chi-restraints excluded: chain Pm residue 160 GLN Chi-restraints excluded: chain Pm residue 190 MET Chi-restraints excluded: chain Pm residue 191 VAL Chi-restraints excluded: chain Ph residue 39 ASN Chi-restraints excluded: chain Ph residue 126 LEU Chi-restraints excluded: chain Pl residue 109 LYS Chi-restraints excluded: chain Pl residue 163 GLU Chi-restraints excluded: chain Pl residue 190 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 245 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 242 optimal weight: 0.8980 chunk 112 optimal weight: 0.1980 chunk 232 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Pb 39 ASN ** Pb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Pe 42 ASN Pa 83 HIS ** Pd 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Pl 39 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.051796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.046661 restraints weight = 47097.671| |-----------------------------------------------------------------------------| r_work (start): 0.2535 rms_B_bonded: 1.51 r_work: 0.2454 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2368 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20236 Z= 0.153 Angle : 0.545 7.249 27315 Z= 0.290 Chirality : 0.044 0.150 3181 Planarity : 0.004 0.040 3561 Dihedral : 5.081 58.672 2769 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.92 % Rotamer: Outliers : 3.21 % Allowed : 14.32 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.16), residues: 2545 helix: 1.87 (0.14), residues: 1388 sheet: -0.12 (0.32), residues: 222 loop : -0.81 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGPc 23 TYR 0.017 0.001 TYRPm 18 PHE 0.009 0.001 PHEPg 50 HIS 0.003 0.001 HISPf 142 Details of bonding type rmsd covalent geometry : bond 0.00367 (20236) covalent geometry : angle 0.54500 (27315) hydrogen bonds : bond 0.03947 ( 1164) hydrogen bonds : angle 3.86606 ( 3639) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 241 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Pb 55 ASP cc_start: 0.8334 (t0) cc_final: 0.8041 (t0) REVERT: Pa 31 MET cc_start: 0.9342 (mmt) cc_final: 0.9127 (mmt) REVERT: Pa 95 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7310 (tpp) REVERT: Pc 27 ASP cc_start: 0.8449 (m-30) cc_final: 0.7876 (m-30) REVERT: Pc 35 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: Pd 18 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7265 (m-80) REVERT: Pd 95 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8070 (tpp) REVERT: Pd 173 ASN cc_start: 0.8587 (t0) cc_final: 0.8340 (t160) REVERT: Pf 18 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.8266 (m-80) REVERT: Pf 26 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8691 (tttp) REVERT: Pq 9 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7126 (mt-10) REVERT: Pq 23 ARG cc_start: 0.6418 (mmt180) cc_final: 0.5036 (tpt90) REVERT: Pq 35 GLN cc_start: 0.8919 (tt0) cc_final: 0.7486 (pp30) REVERT: Pq 99 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7783 (mmp) REVERT: Pi 23 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7861 (tpt-90) REVERT: Pi 95 MET cc_start: 0.9043 (tpt) cc_final: 0.8561 (tpt) REVERT: Pn 27 ASP cc_start: 0.9264 (OUTLIER) cc_final: 0.8745 (m-30) REVERT: Pn 160 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: Pm 62 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8877 (tt) REVERT: Pm 160 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8231 (mp10) outliers start: 69 outliers final: 35 residues processed: 276 average time/residue: 0.8159 time to fit residues: 246.8458 Evaluate side-chains 276 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 228 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Pb residue 18 TYR Chi-restraints excluded: chain Pb residue 162 ILE Chi-restraints excluded: chain Pb residue 191 VAL Chi-restraints excluded: chain Pe residue 40 VAL Chi-restraints excluded: chain Pe residue 119 GLU Chi-restraints excluded: chain Pe residue 162 ILE Chi-restraints excluded: chain Pe residue 185 LEU Chi-restraints excluded: chain Pa residue 7 VAL Chi-restraints excluded: chain Pa residue 79 ASP Chi-restraints excluded: chain Pa residue 95 MET Chi-restraints excluded: chain Pa residue 109 LYS Chi-restraints excluded: chain Pa residue 121 MET Chi-restraints excluded: chain Pa residue 182 GLU Chi-restraints excluded: chain Pc residue 31 MET Chi-restraints excluded: chain Pc residue 35 GLN Chi-restraints excluded: chain Pc residue 191 VAL Chi-restraints excluded: chain Pd residue 18 TYR Chi-restraints excluded: chain Pd residue 95 MET Chi-restraints excluded: chain Pd residue 191 VAL Chi-restraints excluded: chain Pg residue 24 LEU Chi-restraints excluded: chain Pg residue 121 MET Chi-restraints excluded: chain Po residue 162 ILE Chi-restraints excluded: chain Pf residue 18 TYR Chi-restraints excluded: chain Pf residue 26 LYS Chi-restraints excluded: chain Pf residue 193 GLU Chi-restraints excluded: chain Pq residue 9 GLU Chi-restraints excluded: chain Pq residue 99 MET Chi-restraints excluded: chain Pq residue 119 GLU Chi-restraints excluded: chain Pq residue 190 MET Chi-restraints excluded: chain Pi residue 19 ASP Chi-restraints excluded: chain Pi residue 23 ARG Chi-restraints excluded: chain Pi residue 191 VAL Chi-restraints excluded: chain Pn residue 27 ASP Chi-restraints excluded: chain Pn residue 32 LEU Chi-restraints excluded: chain Pn residue 95 MET Chi-restraints excluded: chain Pn residue 119 GLU Chi-restraints excluded: chain Pn residue 160 GLN Chi-restraints excluded: chain Pm residue 7 VAL Chi-restraints excluded: chain Pm residue 62 LEU Chi-restraints excluded: chain Pm residue 72 THR Chi-restraints excluded: chain Pm residue 98 SER Chi-restraints excluded: chain Pm residue 160 GLN Chi-restraints excluded: chain Pm residue 190 MET Chi-restraints excluded: chain Pm residue 191 VAL Chi-restraints excluded: chain Ph residue 39 ASN Chi-restraints excluded: chain Ph residue 126 LEU Chi-restraints excluded: chain Pl residue 163 GLU Chi-restraints excluded: chain Pl residue 190 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 59 optimal weight: 3.9990 chunk 214 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 235 optimal weight: 0.3980 chunk 116 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 148 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Pb 39 ASN ** Pb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Pe 42 ASN Pa 83 HIS Pc 117 ASN ** Pd 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Pf 42 ASN Pm 130 GLN Pl 39 ASN Pl 52 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.052462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.047320 restraints weight = 47053.891| |-----------------------------------------------------------------------------| r_work (start): 0.2552 rms_B_bonded: 1.51 r_work: 0.2472 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2386 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20236 Z= 0.135 Angle : 0.527 7.388 27315 Z= 0.279 Chirality : 0.043 0.149 3181 Planarity : 0.004 0.038 3561 Dihedral : 4.957 59.078 2769 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.08 % Favored : 97.88 % Rotamer: Outliers : 3.30 % Allowed : 14.50 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.17), residues: 2545 helix: 2.03 (0.14), residues: 1386 sheet: -0.15 (0.32), residues: 225 loop : -0.78 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGPc 23 TYR 0.017 0.001 TYRPm 18 PHE 0.009 0.001 PHEPg 50 HIS 0.003 0.001 HISPf 142 Details of bonding type rmsd covalent geometry : bond 0.00319 (20236) covalent geometry : angle 0.52695 (27315) hydrogen bonds : bond 0.03720 ( 1164) hydrogen bonds : angle 3.77560 ( 3639) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 246 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Pb 55 ASP cc_start: 0.8273 (t0) cc_final: 0.8056 (t0) REVERT: Pe 182 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8422 (tm-30) REVERT: Pa 31 MET cc_start: 0.9342 (mmt) cc_final: 0.9066 (mmt) REVERT: Pc 27 ASP cc_start: 0.8407 (m-30) cc_final: 0.7870 (m-30) REVERT: Pc 35 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: Pd 18 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7247 (m-80) REVERT: Pd 95 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8086 (tpp) REVERT: Pd 173 ASN cc_start: 0.8571 (t0) cc_final: 0.8297 (t160) REVERT: Pf 18 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: Pf 26 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8701 (tttp) REVERT: Pq 9 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: Pq 23 ARG cc_start: 0.6409 (mmt180) cc_final: 0.5037 (tpt90) REVERT: Pq 35 GLN cc_start: 0.8865 (tt0) cc_final: 0.7475 (pp30) REVERT: Pq 99 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7864 (mmp) REVERT: Pi 23 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7787 (tpt-90) REVERT: Pi 95 MET cc_start: 0.9029 (tpt) cc_final: 0.8588 (tpt) REVERT: Pi 121 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.8735 (ttm) REVERT: Pn 27 ASP cc_start: 0.9252 (OUTLIER) cc_final: 0.8687 (m-30) REVERT: Pn 160 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.7930 (mp10) REVERT: Pm 62 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8874 (tt) outliers start: 71 outliers final: 33 residues processed: 281 average time/residue: 0.8456 time to fit residues: 260.5473 Evaluate side-chains 286 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Pb residue 18 TYR Chi-restraints excluded: chain Pb residue 154 LEU Chi-restraints excluded: chain Pb residue 162 ILE Chi-restraints excluded: chain Pb residue 191 VAL Chi-restraints excluded: chain Pe residue 40 VAL Chi-restraints excluded: chain Pe residue 119 GLU Chi-restraints excluded: chain Pe residue 162 ILE Chi-restraints excluded: chain Pe residue 182 GLU Chi-restraints excluded: chain Pe residue 185 LEU Chi-restraints excluded: chain Pa residue 7 VAL Chi-restraints excluded: chain Pa residue 109 LYS Chi-restraints excluded: chain Pa residue 121 MET Chi-restraints excluded: chain Pa residue 182 GLU Chi-restraints excluded: chain Pc residue 31 MET Chi-restraints excluded: chain Pc residue 35 GLN Chi-restraints excluded: chain Pc residue 191 VAL Chi-restraints excluded: chain Pd residue 18 TYR Chi-restraints excluded: chain Pd residue 95 MET Chi-restraints excluded: chain Pd residue 191 VAL Chi-restraints excluded: chain Pg residue 31 MET Chi-restraints excluded: chain Pg residue 121 MET Chi-restraints excluded: chain Po residue 162 ILE Chi-restraints excluded: chain Pf residue 18 TYR Chi-restraints excluded: chain Pf residue 26 LYS Chi-restraints excluded: chain Pf residue 193 GLU Chi-restraints excluded: chain Pq residue 9 GLU Chi-restraints excluded: chain Pq residue 99 MET Chi-restraints excluded: chain Pq residue 119 GLU Chi-restraints excluded: chain Pi residue 23 ARG Chi-restraints excluded: chain Pi residue 93 ILE Chi-restraints excluded: chain Pi residue 121 MET Chi-restraints excluded: chain Pi residue 191 VAL Chi-restraints excluded: chain Pn residue 27 ASP Chi-restraints excluded: chain Pn residue 32 LEU Chi-restraints excluded: chain Pn residue 119 GLU Chi-restraints excluded: chain Pn residue 160 GLN Chi-restraints excluded: chain Pm residue 7 VAL Chi-restraints excluded: chain Pm residue 62 LEU Chi-restraints excluded: chain Pm residue 72 THR Chi-restraints excluded: chain Pm residue 98 SER Chi-restraints excluded: chain Pm residue 190 MET Chi-restraints excluded: chain Pm residue 191 VAL Chi-restraints excluded: chain Ph residue 126 LEU Chi-restraints excluded: chain Pl residue 163 GLU Chi-restraints excluded: chain Pl residue 170 ASP Chi-restraints excluded: chain Pl residue 190 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 86 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 253 optimal weight: 0.4980 chunk 177 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 252 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Pb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Pe 42 ASN Pa 83 HIS ** Pd 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Pl 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.052049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.046925 restraints weight = 47160.095| |-----------------------------------------------------------------------------| r_work (start): 0.2542 rms_B_bonded: 1.51 r_work: 0.2461 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2375 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20236 Z= 0.149 Angle : 0.549 9.349 27315 Z= 0.289 Chirality : 0.044 0.156 3181 Planarity : 0.004 0.043 3561 Dihedral : 4.923 58.558 2767 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.92 % Rotamer: Outliers : 3.11 % Allowed : 15.57 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.16), residues: 2545 helix: 1.97 (0.14), residues: 1385 sheet: -0.15 (0.32), residues: 225 loop : -0.80 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGPc 23 TYR 0.016 0.001 TYRPm 18 PHE 0.009 0.001 PHEPg 50 HIS 0.003 0.001 HISPf 142 Details of bonding type rmsd covalent geometry : bond 0.00357 (20236) covalent geometry : angle 0.54853 (27315) hydrogen bonds : bond 0.03870 ( 1164) hydrogen bonds : angle 3.80856 ( 3639) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 246 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: Pe 182 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8385 (tm-30) REVERT: Pa 31 MET cc_start: 0.9346 (mmt) cc_final: 0.9069 (mmt) REVERT: Pc 27 ASP cc_start: 0.8432 (m-30) cc_final: 0.7855 (m-30) REVERT: Pc 35 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: Pd 18 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7270 (m-80) REVERT: Pd 95 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8085 (tpp) REVERT: Pd 173 ASN cc_start: 0.8578 (t0) cc_final: 0.8295 (t160) REVERT: Pg 18 TYR cc_start: 0.9196 (m-80) cc_final: 0.8921 (m-80) REVERT: Pf 18 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8192 (m-80) REVERT: Pf 26 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8698 (tttp) REVERT: Pq 9 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7114 (mt-10) REVERT: Pq 23 ARG cc_start: 0.6428 (mmt180) cc_final: 0.5036 (tpt90) REVERT: Pq 35 GLN cc_start: 0.8915 (tt0) cc_final: 0.7506 (pp30) REVERT: Pq 99 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7830 (mmp) REVERT: Pi 23 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7798 (tpt-90) REVERT: Pi 121 MET cc_start: 0.9357 (OUTLIER) cc_final: 0.8746 (ttm) REVERT: Pn 27 ASP cc_start: 0.9272 (OUTLIER) cc_final: 0.8744 (m-30) REVERT: Pm 62 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8855 (tt) REVERT: Ph 121 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.8609 (ttp) REVERT: Pl 8 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7427 (pt) REVERT: Pl 85 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8349 (mtpt) outliers start: 67 outliers final: 36 residues processed: 278 average time/residue: 0.8304 time to fit residues: 253.1315 Evaluate side-chains 283 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Pb residue 10 THR Chi-restraints excluded: chain Pb residue 18 TYR Chi-restraints excluded: chain Pb residue 154 LEU Chi-restraints excluded: chain Pb residue 162 ILE Chi-restraints excluded: chain Pb residue 191 VAL Chi-restraints excluded: chain Pe residue 40 VAL Chi-restraints excluded: chain Pe residue 119 GLU Chi-restraints excluded: chain Pe residue 162 ILE Chi-restraints excluded: chain Pe residue 182 GLU Chi-restraints excluded: chain Pe residue 185 LEU Chi-restraints excluded: chain Pa residue 7 VAL Chi-restraints excluded: chain Pa residue 109 LYS Chi-restraints excluded: chain Pa residue 121 MET Chi-restraints excluded: chain Pa residue 182 GLU Chi-restraints excluded: chain Pc residue 31 MET Chi-restraints excluded: chain Pc residue 35 GLN Chi-restraints excluded: chain Pc residue 191 VAL Chi-restraints excluded: chain Pd residue 18 TYR Chi-restraints excluded: chain Pd residue 95 MET Chi-restraints excluded: chain Pd residue 191 VAL Chi-restraints excluded: chain Pg residue 31 MET Chi-restraints excluded: chain Pg residue 121 MET Chi-restraints excluded: chain Po residue 162 ILE Chi-restraints excluded: chain Pf residue 18 TYR Chi-restraints excluded: chain Pf residue 26 LYS Chi-restraints excluded: chain Pq residue 9 GLU Chi-restraints excluded: chain Pq residue 99 MET Chi-restraints excluded: chain Pq residue 119 GLU Chi-restraints excluded: chain Pi residue 23 ARG Chi-restraints excluded: chain Pi residue 93 ILE Chi-restraints excluded: chain Pi residue 121 MET Chi-restraints excluded: chain Pi residue 191 VAL Chi-restraints excluded: chain Pn residue 27 ASP Chi-restraints excluded: chain Pn residue 32 LEU Chi-restraints excluded: chain Pn residue 35 GLN Chi-restraints excluded: chain Pn residue 119 GLU Chi-restraints excluded: chain Pm residue 7 VAL Chi-restraints excluded: chain Pm residue 62 LEU Chi-restraints excluded: chain Pm residue 72 THR Chi-restraints excluded: chain Pm residue 98 SER Chi-restraints excluded: chain Pm residue 167 LYS Chi-restraints excluded: chain Pm residue 190 MET Chi-restraints excluded: chain Pm residue 191 VAL Chi-restraints excluded: chain Ph residue 39 ASN Chi-restraints excluded: chain Ph residue 121 MET Chi-restraints excluded: chain Ph residue 126 LEU Chi-restraints excluded: chain Pl residue 8 ILE Chi-restraints excluded: chain Pl residue 163 GLU Chi-restraints excluded: chain Pl residue 170 ASP Chi-restraints excluded: chain Pl residue 190 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 100 optimal weight: 0.8980 chunk 88 optimal weight: 0.4980 chunk 120 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Pb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Pe 42 ASN Pc 117 ASN ** Pd 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Pn 160 GLN Pl 39 ASN ** Pl 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.051903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.046780 restraints weight = 46772.736| |-----------------------------------------------------------------------------| r_work (start): 0.2538 rms_B_bonded: 1.51 r_work: 0.2458 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2373 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20236 Z= 0.155 Angle : 0.558 7.548 27315 Z= 0.294 Chirality : 0.044 0.155 3181 Planarity : 0.004 0.044 3561 Dihedral : 4.761 42.564 2764 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.56 % Allowed : 16.13 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.16), residues: 2545 helix: 1.93 (0.14), residues: 1386 sheet: -0.15 (0.32), residues: 225 loop : -0.84 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGPc 23 TYR 0.017 0.001 TYRPm 18 PHE 0.009 0.001 PHEPg 50 HIS 0.003 0.001 HISPa 123 Details of bonding type rmsd covalent geometry : bond 0.00373 (20236) covalent geometry : angle 0.55819 (27315) hydrogen bonds : bond 0.03927 ( 1164) hydrogen bonds : angle 3.83693 ( 3639) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 238 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: Pe 182 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8380 (tm-30) REVERT: Pa 31 MET cc_start: 0.9347 (mmt) cc_final: 0.9067 (mmt) REVERT: Pc 27 ASP cc_start: 0.8447 (m-30) cc_final: 0.7865 (m-30) REVERT: Pc 35 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: Pd 18 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.7175 (m-80) REVERT: Pd 95 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8063 (tpp) REVERT: Pd 173 ASN cc_start: 0.8571 (t0) cc_final: 0.8315 (t160) REVERT: Pf 18 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.8239 (m-80) REVERT: Pf 26 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8686 (tttp) REVERT: Pq 9 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7090 (mt-10) REVERT: Pq 23 ARG cc_start: 0.6299 (mmt180) cc_final: 0.4958 (tpt90) REVERT: Pq 35 GLN cc_start: 0.8932 (tt0) cc_final: 0.7526 (pp30) REVERT: Pq 99 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7783 (mmp) REVERT: Pi 23 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7857 (tpt-90) REVERT: Pi 121 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.8752 (ttm) REVERT: Pn 27 ASP cc_start: 0.9277 (OUTLIER) cc_final: 0.8751 (m-30) REVERT: Pm 62 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8853 (tt) REVERT: Ph 121 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8614 (ttp) REVERT: Pl 8 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7460 (pt) outliers start: 55 outliers final: 36 residues processed: 264 average time/residue: 0.8415 time to fit residues: 243.3731 Evaluate side-chains 284 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 234 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Pb residue 10 THR Chi-restraints excluded: chain Pb residue 18 TYR Chi-restraints excluded: chain Pb residue 154 LEU Chi-restraints excluded: chain Pb residue 162 ILE Chi-restraints excluded: chain Pb residue 191 VAL Chi-restraints excluded: chain Pe residue 40 VAL Chi-restraints excluded: chain Pe residue 119 GLU Chi-restraints excluded: chain Pe residue 162 ILE Chi-restraints excluded: chain Pe residue 182 GLU Chi-restraints excluded: chain Pe residue 185 LEU Chi-restraints excluded: chain Pa residue 7 VAL Chi-restraints excluded: chain Pa residue 109 LYS Chi-restraints excluded: chain Pa residue 121 MET Chi-restraints excluded: chain Pa residue 182 GLU Chi-restraints excluded: chain Pc residue 31 MET Chi-restraints excluded: chain Pc residue 35 GLN Chi-restraints excluded: chain Pc residue 191 VAL Chi-restraints excluded: chain Pd residue 18 TYR Chi-restraints excluded: chain Pd residue 95 MET Chi-restraints excluded: chain Pd residue 191 VAL Chi-restraints excluded: chain Pg residue 31 MET Chi-restraints excluded: chain Pg residue 121 MET Chi-restraints excluded: chain Po residue 162 ILE Chi-restraints excluded: chain Pf residue 18 TYR Chi-restraints excluded: chain Pf residue 26 LYS Chi-restraints excluded: chain Pq residue 9 GLU Chi-restraints excluded: chain Pq residue 99 MET Chi-restraints excluded: chain Pq residue 119 GLU Chi-restraints excluded: chain Pi residue 23 ARG Chi-restraints excluded: chain Pi residue 93 ILE Chi-restraints excluded: chain Pi residue 121 MET Chi-restraints excluded: chain Pi residue 191 VAL Chi-restraints excluded: chain Pn residue 27 ASP Chi-restraints excluded: chain Pn residue 32 LEU Chi-restraints excluded: chain Pn residue 35 GLN Chi-restraints excluded: chain Pn residue 119 GLU Chi-restraints excluded: chain Pm residue 7 VAL Chi-restraints excluded: chain Pm residue 62 LEU Chi-restraints excluded: chain Pm residue 72 THR Chi-restraints excluded: chain Pm residue 98 SER Chi-restraints excluded: chain Pm residue 167 LYS Chi-restraints excluded: chain Pm residue 190 MET Chi-restraints excluded: chain Pm residue 191 VAL Chi-restraints excluded: chain Ph residue 39 ASN Chi-restraints excluded: chain Ph residue 121 MET Chi-restraints excluded: chain Ph residue 126 LEU Chi-restraints excluded: chain Pl residue 8 ILE Chi-restraints excluded: chain Pl residue 163 GLU Chi-restraints excluded: chain Pl residue 170 ASP Chi-restraints excluded: chain Pl residue 190 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 173 optimal weight: 1.9990 chunk 216 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 212 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Pb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Pe 42 ASN ** Pd 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Pl 39 ASN ** Pl 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.051968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.046837 restraints weight = 47095.914| |-----------------------------------------------------------------------------| r_work (start): 0.2539 rms_B_bonded: 1.51 r_work: 0.2459 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2373 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20236 Z= 0.152 Angle : 0.558 8.923 27315 Z= 0.293 Chirality : 0.044 0.154 3181 Planarity : 0.004 0.045 3561 Dihedral : 4.757 42.570 2764 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.51 % Allowed : 16.41 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.16), residues: 2545 helix: 1.95 (0.14), residues: 1386 sheet: -0.27 (0.32), residues: 217 loop : -0.79 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGPc 23 TYR 0.018 0.001 TYRPm 18 PHE 0.009 0.001 PHEPg 50 HIS 0.003 0.001 HISPf 142 Details of bonding type rmsd covalent geometry : bond 0.00366 (20236) covalent geometry : angle 0.55762 (27315) hydrogen bonds : bond 0.03893 ( 1164) hydrogen bonds : angle 3.83615 ( 3639) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5090 Ramachandran restraints generated. 2545 Oldfield, 0 Emsley, 2545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 239 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Pa 31 MET cc_start: 0.9345 (mmt) cc_final: 0.9071 (mmt) REVERT: Pc 27 ASP cc_start: 0.8431 (m-30) cc_final: 0.8144 (m-30) REVERT: Pc 35 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: Pd 18 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7168 (m-80) REVERT: Pd 95 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8081 (tpp) REVERT: Pd 173 ASN cc_start: 0.8576 (t0) cc_final: 0.8280 (t160) REVERT: Pf 18 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8267 (m-80) REVERT: Pf 26 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8688 (tttp) REVERT: Pq 9 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: Pq 23 ARG cc_start: 0.6296 (mmt180) cc_final: 0.4952 (tpt90) REVERT: Pq 35 GLN cc_start: 0.8925 (tt0) cc_final: 0.7502 (pp30) REVERT: Pq 99 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7780 (mmp) REVERT: Pi 23 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7794 (tpt-90) REVERT: Pi 95 MET cc_start: 0.8954 (tpt) cc_final: 0.8515 (tpt) REVERT: Pi 121 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.8762 (ttm) REVERT: Pn 27 ASP cc_start: 0.9275 (OUTLIER) cc_final: 0.8741 (m-30) REVERT: Pm 62 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8858 (tt) REVERT: Ph 121 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8616 (ttp) REVERT: Pl 8 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7486 (pt) REVERT: Pl 85 LYS cc_start: 0.8670 (mtmm) cc_final: 0.8438 (mtpt) outliers start: 54 outliers final: 39 residues processed: 266 average time/residue: 0.8271 time to fit residues: 240.9713 Evaluate side-chains 279 residues out of total 2153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 227 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Pb residue 10 THR Chi-restraints excluded: chain Pb residue 18 TYR Chi-restraints excluded: chain Pb residue 154 LEU Chi-restraints excluded: chain Pb residue 162 ILE Chi-restraints excluded: chain Pb residue 191 VAL Chi-restraints excluded: chain Pe residue 40 VAL Chi-restraints excluded: chain Pe residue 119 GLU Chi-restraints excluded: chain Pe residue 162 ILE Chi-restraints excluded: chain Pe residue 185 LEU Chi-restraints excluded: chain Pa residue 7 VAL Chi-restraints excluded: chain Pa residue 83 HIS Chi-restraints excluded: chain Pa residue 109 LYS Chi-restraints excluded: chain Pa residue 121 MET Chi-restraints excluded: chain Pa residue 182 GLU Chi-restraints excluded: chain Pc residue 8 ILE Chi-restraints excluded: chain Pc residue 31 MET Chi-restraints excluded: chain Pc residue 35 GLN Chi-restraints excluded: chain Pc residue 191 VAL Chi-restraints excluded: chain Pd residue 8 ILE Chi-restraints excluded: chain Pd residue 18 TYR Chi-restraints excluded: chain Pd residue 95 MET Chi-restraints excluded: chain Pd residue 191 VAL Chi-restraints excluded: chain Pg residue 31 MET Chi-restraints excluded: chain Pg residue 121 MET Chi-restraints excluded: chain Po residue 162 ILE Chi-restraints excluded: chain Pf residue 18 TYR Chi-restraints excluded: chain Pf residue 26 LYS Chi-restraints excluded: chain Pq residue 9 GLU Chi-restraints excluded: chain Pq residue 99 MET Chi-restraints excluded: chain Pq residue 119 GLU Chi-restraints excluded: chain Pi residue 23 ARG Chi-restraints excluded: chain Pi residue 93 ILE Chi-restraints excluded: chain Pi residue 121 MET Chi-restraints excluded: chain Pi residue 191 VAL Chi-restraints excluded: chain Pn residue 27 ASP Chi-restraints excluded: chain Pn residue 32 LEU Chi-restraints excluded: chain Pn residue 35 GLN Chi-restraints excluded: chain Pn residue 119 GLU Chi-restraints excluded: chain Pm residue 7 VAL Chi-restraints excluded: chain Pm residue 62 LEU Chi-restraints excluded: chain Pm residue 72 THR Chi-restraints excluded: chain Pm residue 98 SER Chi-restraints excluded: chain Pm residue 167 LYS Chi-restraints excluded: chain Pm residue 190 MET Chi-restraints excluded: chain Pm residue 191 VAL Chi-restraints excluded: chain Ph residue 39 ASN Chi-restraints excluded: chain Ph residue 121 MET Chi-restraints excluded: chain Ph residue 126 LEU Chi-restraints excluded: chain Pl residue 8 ILE Chi-restraints excluded: chain Pl residue 163 GLU Chi-restraints excluded: chain Pl residue 170 ASP Chi-restraints excluded: chain Pl residue 190 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 70 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 181 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Pb 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Pe 42 ASN Pc 117 ASN ** Pd 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Pl 39 ASN ** Pl 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.052235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.047089 restraints weight = 47426.060| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 1.52 r_work: 0.2467 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2380 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20236 Z= 0.145 Angle : 0.556 7.852 27315 Z= 0.291 Chirality : 0.043 0.153 3181 Planarity : 0.004 0.047 3561 Dihedral : 4.730 42.731 2764 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.65 % Allowed : 16.27 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.16), residues: 2545 helix: 1.99 (0.14), residues: 1385 sheet: -0.26 (0.32), residues: 217 loop : -0.79 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGPc 23 TYR 0.018 0.001 TYRPm 18 PHE 0.009 0.001 PHEPg 50 HIS 0.003 0.001 HISPf 142 Details of bonding type rmsd covalent geometry : bond 0.00347 (20236) covalent geometry : angle 0.55580 (27315) hydrogen bonds : bond 0.03807 ( 1164) hydrogen bonds : angle 3.80403 ( 3639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6439.12 seconds wall clock time: 110 minutes 34.66 seconds (6634.66 seconds total)