Starting phenix.real_space_refine on Fri Feb 6 15:02:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vf2_43184/02_2026/8vf2_43184.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vf2_43184/02_2026/8vf2_43184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vf2_43184/02_2026/8vf2_43184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vf2_43184/02_2026/8vf2_43184.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vf2_43184/02_2026/8vf2_43184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vf2_43184/02_2026/8vf2_43184.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 6 Type Number sf(0) Gaussians P 118 5.49 5 S 66 5.16 5 C 8025 2.51 5 N 2349 2.21 5 O 2799 1.98 5 H 12066 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s 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: 25423 Number of models: 1 Model: "" Number of chains: 10 Chain: "I" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 683 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "J" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 708 Classifications: {'DNA': 22} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 3605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3605 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain: "B" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3625 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain: "C" Number of atoms: 3605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3605 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain: "D" Number of atoms: 3624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3624 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain: "E" Number of atoms: 3605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3605 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain: "F" Number of atoms: 3624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3624 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain: "G" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1167 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} Chain: "H" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 1177 Classifications: {'DNA': 37} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 36} Time building chain proxies: 4.62, per 1000 atoms: 0.18 Number of scatterers: 25423 At special positions: 0 Unit cell: (89.964, 89.964, 208.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 118 15.00 O 2799 8.00 N 2349 7.00 C 8025 6.00 H 12066 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 51 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 51 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 51 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 909.9 milliseconds 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2622 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 14 sheets defined 30.4% alpha, 22.4% beta 54 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 4.80 Creating SS restraints... Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.571A pdb=" N ILE A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 82 No H-bonds generated for 'chain 'A' and resid 81 through 82' Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 119 through 133 Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.654A pdb=" N MET A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 213 through 226 Processing helix chain 'B' and resid 75 through 82 removed outlier: 4.261A pdb=" N ILE B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 118 through 133 removed outlier: 3.577A pdb=" N TYR B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 4.018A pdb=" N ASP B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN B 183 " --> pdb=" O PRO B 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 178 through 183' Processing helix chain 'B' and resid 188 through 201 removed outlier: 3.797A pdb=" N LEU B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS B 193 " --> pdb=" O PRO B 189 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN B 197 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 198 " --> pdb=" O MET B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 227 Processing helix chain 'C' and resid 75 through 80 removed outlier: 4.073A pdb=" N ILE C 79 " --> pdb=" O THR C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 118 through 133 removed outlier: 4.586A pdb=" N TYR C 122 " --> pdb=" O SER C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 Processing helix chain 'C' and resid 178 through 183 removed outlier: 4.057A pdb=" N ASP C 182 " --> pdb=" O PHE C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 203 removed outlier: 3.522A pdb=" N MET C 202 " --> pdb=" O VAL C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 213 through 226 removed outlier: 3.730A pdb=" N LYS C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 115 through 117 No H-bonds generated for 'chain 'D' and resid 115 through 117' Processing helix chain 'D' and resid 118 through 133 Processing helix chain 'D' and resid 169 through 173 Processing helix chain 'D' and resid 178 through 183 removed outlier: 4.001A pdb=" N ASP D 182 " --> pdb=" O PHE D 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 178 through 183' Processing helix chain 'D' and resid 188 through 201 Processing helix chain 'D' and resid 213 through 227 removed outlier: 3.923A pdb=" N LEU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 75 through 80 removed outlier: 3.916A pdb=" N ILE E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 86 removed outlier: 6.239A pdb=" N GLU E 84 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU E 85 " --> pdb=" O LEU E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 101 No H-bonds generated for 'chain 'E' and resid 99 through 101' Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 118 through 133 removed outlier: 4.117A pdb=" N TYR E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 173 removed outlier: 3.501A pdb=" N ILE E 173 " --> pdb=" O PRO E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 183 removed outlier: 4.176A pdb=" N LEU E 181 " --> pdb=" O PHE E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 201 removed outlier: 4.485A pdb=" N GLN E 197 " --> pdb=" O LYS E 193 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL E 198 " --> pdb=" O MET E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 226 Processing helix chain 'F' and resid 75 through 81 Processing helix chain 'F' and resid 99 through 101 No H-bonds generated for 'chain 'F' and resid 99 through 101' Processing helix chain 'F' and resid 119 through 133 removed outlier: 4.162A pdb=" N LEU F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 202 removed outlier: 3.867A pdb=" N LEU F 192 " --> pdb=" O LYS F 188 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS F 193 " --> pdb=" O PRO F 189 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET F 202 " --> pdb=" O VAL F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 227 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 removed outlier: 3.680A pdb=" N PHE A 11 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 10 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 22 removed outlier: 6.293A pdb=" N VAL A 153 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ARG A 134 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.584A pdb=" N TYR B 64 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 72 " --> pdb=" O TYR B 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 48 removed outlier: 4.321A pdb=" N ILE B 42 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLN B 33 " --> pdb=" O ILE B 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 7 through 9 removed outlier: 3.877A pdb=" N ARG B 108 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N MET B 162 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 161 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 149 " --> pdb=" O VAL B 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 5 through 9 removed outlier: 4.149A pdb=" N TRP C 5 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 161 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL C 153 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N ARG C 134 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU C 94 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N HIS C 139 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL C 92 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N THR C 141 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE C 90 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N ILE C 90 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER C 8 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL C 92 " --> pdb=" O SER C 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 40 through 41 removed outlier: 3.742A pdb=" N GLY C 40 " --> pdb=" O HIS C 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 48 removed outlier: 3.701A pdb=" N LYS C 45 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY D 40 " --> pdb=" O HIS D 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 7 through 9 removed outlier: 6.326A pdb=" N THR D 166 " --> pdb=" O ASP D 107 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER D 109 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL D 164 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE D 111 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N MET D 162 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N GLU D 113 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 12.744A pdb=" N GLU D 160 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU D 148 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL D 138 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL D 153 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ARG D 134 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU D 94 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N HIS D 139 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL D 92 " --> pdb=" O HIS D 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 5 through 8 removed outlier: 3.617A pdb=" N TRP E 5 " --> pdb=" O VAL E 20 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 43 through 48 removed outlier: 3.836A pdb=" N GLY E 40 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE E 42 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN E 33 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 12.388A pdb=" N TYR E 44 " --> pdb=" O PHE E 31 " (cutoff:3.500A) removed outlier: 17.229A pdb=" N PHE E 31 " --> pdb=" O TYR E 44 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL E 34 " --> pdb=" O ALA F 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 62 through 63 removed outlier: 3.861A pdb=" N ALA E 63 " --> pdb=" O HIS F 32 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS F 35 " --> pdb=" O GLY F 40 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY F 40 " --> pdb=" O HIS F 35 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 92 through 97 removed outlier: 7.421A pdb=" N VAL E 92 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N HIS E 139 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU E 94 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N ARG E 134 " --> pdb=" O VAL E 153 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL E 153 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU E 148 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG E 108 " --> pdb=" O THR E 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 89 through 90 removed outlier: 8.031A pdb=" N ILE F 90 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER F 8 " --> pdb=" O ILE F 90 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TRP F 5 " --> pdb=" O VAL F 20 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG F 108 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N MET F 162 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL F 161 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU F 148 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL F 153 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ARG F 134 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU F 94 " --> pdb=" O ILE F 137 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 147 hydrogen bonds 290 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 6.60 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 12066 1.04 - 1.23: 175 1.23 - 1.43: 5957 1.43 - 1.63: 7612 1.63 - 1.82: 120 Bond restraints: 25930 Sorted by residual: bond pdb=" N ILE A 29 " pdb=" H ILE A 29 " ideal model delta sigma weight residual 0.860 0.972 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" N ASP A 28 " pdb=" H ASP A 28 " ideal model delta sigma weight residual 0.860 0.971 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" N TYR A 57 " pdb=" H TYR A 57 " ideal model delta sigma weight residual 0.860 0.971 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" N ASP A 56 " pdb=" H ASP A 56 " ideal model delta sigma weight residual 0.860 0.968 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 ... (remaining 25925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 15.13: 46897 15.13 - 30.27: 0 30.27 - 45.40: 0 45.40 - 60.53: 0 60.53 - 75.66: 2 Bond angle restraints: 46899 Sorted by residual: angle pdb=" C ASP A 28 " pdb=" N ILE A 29 " pdb=" H ILE A 29 " ideal model delta sigma weight residual 123.96 48.30 75.66 3.00e+00 1.11e-01 6.36e+02 angle pdb=" C VAL A 55 " pdb=" N ASP A 56 " pdb=" H ASP A 56 " ideal model delta sigma weight residual 124.67 50.59 74.08 3.00e+00 1.11e-01 6.10e+02 angle pdb=" CA LYS C 37 " pdb=" CB LYS C 37 " pdb=" CG LYS C 37 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CB MET A 1 " pdb=" CG MET A 1 " pdb=" SD MET A 1 " ideal model delta sigma weight residual 112.70 120.79 -8.09 3.00e+00 1.11e-01 7.28e+00 angle pdb=" CA ILE A 29 " pdb=" N ILE A 29 " pdb=" H ILE A 29 " ideal model delta sigma weight residual 113.66 106.36 7.31 3.00e+00 1.11e-01 5.93e+00 ... (remaining 46894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.97: 10586 31.97 - 63.94: 1043 63.94 - 95.90: 44 95.90 - 127.87: 0 127.87 - 159.84: 2 Dihedral angle restraints: 11675 sinusoidal: 7009 harmonic: 4666 Sorted by residual: dihedral pdb=" CB CYS C 48 " pdb=" SG CYS C 48 " pdb=" SG CYS C 51 " pdb=" CB CYS C 51 " ideal model delta sinusoidal sigma weight residual 93.00 146.83 -53.83 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" CB CYS A 48 " pdb=" SG CYS A 48 " pdb=" SG CYS A 51 " pdb=" CB CYS A 51 " ideal model delta sinusoidal sigma weight residual 93.00 137.81 -44.81 1 1.00e+01 1.00e-02 2.79e+01 dihedral pdb=" CA ARG B 134 " pdb=" C ARG B 134 " pdb=" N MET B 135 " pdb=" CA MET B 135 " ideal model delta harmonic sigma weight residual 180.00 159.56 20.44 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 11672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1288 0.028 - 0.057: 518 0.057 - 0.085: 162 0.085 - 0.113: 137 0.113 - 0.141: 35 Chirality restraints: 2140 Sorted by residual: chirality pdb=" C1' DC I 3 " pdb=" O4' DC I 3 " pdb=" C2' DC I 3 " pdb=" N1 DC I 3 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA VAL D 96 " pdb=" N VAL D 96 " pdb=" C VAL D 96 " pdb=" CB VAL D 96 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE D 9 " pdb=" N ILE D 9 " pdb=" C ILE D 9 " pdb=" CB ILE D 9 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 2137 not shown) Planarity restraints: 3490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 28 " 0.119 2.00e-02 2.50e+03 2.75e-01 7.54e+02 pdb=" N ILE A 29 " -0.474 2.00e-02 2.50e+03 pdb=" CA ILE A 29 " 0.180 2.00e-02 2.50e+03 pdb=" H ILE A 29 " 0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 55 " 0.107 2.00e-02 2.50e+03 2.68e-01 7.21e+02 pdb=" N ASP A 56 " -0.462 2.00e-02 2.50e+03 pdb=" CA ASP A 56 " 0.172 2.00e-02 2.50e+03 pdb=" H ASP A 56 " 0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 27 " 0.025 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" C HIS A 27 " -0.087 2.00e-02 2.50e+03 pdb=" O HIS A 27 " 0.033 2.00e-02 2.50e+03 pdb=" N ASP A 28 " 0.028 2.00e-02 2.50e+03 ... (remaining 3487 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1484 2.18 - 2.78: 48496 2.78 - 3.39: 69550 3.39 - 3.99: 90787 3.99 - 4.60: 134691 Nonbonded interactions: 345008 Sorted by model distance: nonbonded pdb=" O ARG C 210 " pdb="HH11 ARG C 210 " model vdw 1.572 2.450 nonbonded pdb=" HG SER C 8 " pdb=" OD1 ASN C 15 " model vdw 1.601 2.450 nonbonded pdb=" O HIS E 35 " pdb=" H ASN E 39 " model vdw 1.615 2.450 nonbonded pdb="HH22 ARG B 58 " pdb=" OP1 DC G 13 " model vdw 1.632 2.450 nonbonded pdb=" O VAL F 198 " pdb=" HG SER F 201 " model vdw 1.637 2.450 ... (remaining 345003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE \ 1)) or resid 28 through 226)) selection = chain 'C' selection = (chain 'D' and resid 1 through 226) selection = chain 'E' selection = (chain 'F' and resid 1 through 226) } 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 group one per residue 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: 7.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.170 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.750 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 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 : 0.003 0.036 13870 Z= 0.136 Angle : 0.558 8.095 19272 Z= 0.314 Chirality : 0.042 0.141 2140 Planarity : 0.004 0.051 2095 Dihedral : 22.679 159.838 5465 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.34 % Allowed : 30.73 % Favored : 68.93 % 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: -0.31 (0.23), residues: 1347 helix: 1.31 (0.31), residues: 284 sheet: -1.26 (0.33), residues: 263 loop : -0.31 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 62 TYR 0.013 0.001 TYR A 215 PHE 0.008 0.001 PHE B 178 TRP 0.010 0.001 TRP D 5 HIS 0.008 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00295 (13864) covalent geometry : angle 0.55496 (19260) SS BOND : bond 0.00191 ( 6) SS BOND : angle 2.21385 ( 12) hydrogen bonds : bond 0.22027 ( 541) hydrogen bonds : angle 8.65380 ( 1334) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 183 GLN cc_start: 0.5806 (tm-30) cc_final: 0.5388 (tm-30) outliers start: 4 outliers final: 4 residues processed: 184 average time/residue: 0.2194 time to fit residues: 61.0802 Evaluate side-chains 173 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 169 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain F residue 5 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.194683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.133850 restraints weight = 57455.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.137440 restraints weight = 29690.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.139560 restraints weight = 20584.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.141429 restraints weight = 19434.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.142145 restraints weight = 16463.789| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 13870 Z= 0.239 Angle : 0.639 6.368 19272 Z= 0.362 Chirality : 0.046 0.166 2140 Planarity : 0.005 0.055 2095 Dihedral : 23.542 160.635 2742 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.61 % Allowed : 27.79 % Favored : 68.60 % 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: -0.58 (0.23), residues: 1347 helix: 1.16 (0.30), residues: 300 sheet: -1.40 (0.30), residues: 298 loop : -0.52 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 210 TYR 0.021 0.002 TYR B 110 PHE 0.016 0.002 PHE A 11 TRP 0.016 0.002 TRP F 5 HIS 0.007 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00538 (13864) covalent geometry : angle 0.63539 (19260) SS BOND : bond 0.00366 ( 6) SS BOND : angle 2.85365 ( 12) hydrogen bonds : bond 0.06027 ( 541) hydrogen bonds : angle 6.42858 ( 1334) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.7591 (mp) REVERT: B 93 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8533 (mp) REVERT: C 104 MET cc_start: 0.5711 (mmt) cc_final: 0.4895 (mmt) REVERT: F 162 MET cc_start: 0.7458 (mtt) cc_final: 0.7215 (mtt) outliers start: 43 outliers final: 31 residues processed: 200 average time/residue: 0.2214 time to fit residues: 67.1798 Evaluate side-chains 192 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 139 HIS Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 15 ASN Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain F residue 5 TRP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 64 TYR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 141 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 65 optimal weight: 0.0010 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.197950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.137978 restraints weight = 56735.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.142096 restraints weight = 27605.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.144458 restraints weight = 20341.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.146293 restraints weight = 16735.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.146355 restraints weight = 14587.440| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13870 Z= 0.147 Angle : 0.573 6.370 19272 Z= 0.325 Chirality : 0.043 0.155 2140 Planarity : 0.004 0.045 2095 Dihedral : 23.490 159.339 2739 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.19 % Allowed : 28.30 % Favored : 68.51 % 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: -0.43 (0.23), residues: 1347 helix: 1.41 (0.30), residues: 300 sheet: -1.36 (0.30), residues: 293 loop : -0.45 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 143 TYR 0.014 0.001 TYR B 122 PHE 0.010 0.001 PHE F 140 TRP 0.015 0.001 TRP F 5 HIS 0.008 0.001 HIS E 212 Details of bonding type rmsd covalent geometry : bond 0.00329 (13864) covalent geometry : angle 0.56959 (19260) SS BOND : bond 0.00353 ( 6) SS BOND : angle 2.47469 ( 12) hydrogen bonds : bond 0.05135 ( 541) hydrogen bonds : angle 5.87640 ( 1334) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 MET cc_start: 0.5921 (mtp) cc_final: 0.5698 (mtp) REVERT: E 152 ARG cc_start: 0.7967 (ptt90) cc_final: 0.7562 (ptt90) REVERT: F 162 MET cc_start: 0.7535 (mtt) cc_final: 0.7113 (mtt) outliers start: 38 outliers final: 29 residues processed: 200 average time/residue: 0.2422 time to fit residues: 72.0000 Evaluate side-chains 191 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 139 HIS Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain F residue 5 TRP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 151 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 134 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 22 optimal weight: 0.0570 chunk 90 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.197407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.136584 restraints weight = 56469.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.140149 restraints weight = 29281.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.142217 restraints weight = 19272.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.144592 restraints weight = 18783.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.144538 restraints weight = 15441.348| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13870 Z= 0.153 Angle : 0.567 6.107 19272 Z= 0.321 Chirality : 0.043 0.152 2140 Planarity : 0.004 0.046 2095 Dihedral : 23.460 159.456 2739 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.53 % Allowed : 26.78 % Favored : 68.68 % 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: -0.32 (0.23), residues: 1347 helix: 1.61 (0.30), residues: 288 sheet: -1.31 (0.32), residues: 262 loop : -0.45 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 143 TYR 0.012 0.001 TYR B 122 PHE 0.010 0.001 PHE F 140 TRP 0.015 0.001 TRP F 5 HIS 0.004 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00346 (13864) covalent geometry : angle 0.56372 (19260) SS BOND : bond 0.00321 ( 6) SS BOND : angle 2.39726 ( 12) hydrogen bonds : bond 0.04855 ( 541) hydrogen bonds : angle 5.61424 ( 1334) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 169 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.7547 (mp) REVERT: B 142 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7399 (tp) REVERT: D 91 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8016 (pt0) REVERT: E 21 TYR cc_start: 0.7613 (m-10) cc_final: 0.7381 (m-10) REVERT: E 92 VAL cc_start: 0.7468 (OUTLIER) cc_final: 0.7143 (p) REVERT: E 152 ARG cc_start: 0.7954 (ptt90) cc_final: 0.7692 (ptt90) REVERT: F 162 MET cc_start: 0.7569 (mtt) cc_final: 0.7132 (mtt) outliers start: 54 outliers final: 41 residues processed: 207 average time/residue: 0.2344 time to fit residues: 73.4590 Evaluate side-chains 208 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 139 HIS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain F residue 5 TRP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 151 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 63 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 0.0000 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.195604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.135558 restraints weight = 56357.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.138482 restraints weight = 29500.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.140911 restraints weight = 20217.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.142511 restraints weight = 19126.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.142649 restraints weight = 16115.863| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13870 Z= 0.185 Angle : 0.580 6.150 19272 Z= 0.329 Chirality : 0.044 0.161 2140 Planarity : 0.005 0.058 2095 Dihedral : 23.458 159.733 2739 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.04 % Allowed : 26.03 % Favored : 68.93 % 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: -0.35 (0.23), residues: 1347 helix: 1.60 (0.30), residues: 288 sheet: -1.38 (0.32), residues: 262 loop : -0.46 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 143 TYR 0.014 0.001 TYR B 110 PHE 0.016 0.001 PHE F 206 TRP 0.016 0.001 TRP F 5 HIS 0.005 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00418 (13864) covalent geometry : angle 0.57684 (19260) SS BOND : bond 0.00254 ( 6) SS BOND : angle 2.34209 ( 12) hydrogen bonds : bond 0.04908 ( 541) hydrogen bonds : angle 5.54573 ( 1334) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 166 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6066 (mmm) cc_final: 0.5744 (mmm) REVERT: A 167 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.7612 (mp) REVERT: D 91 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8059 (pt0) REVERT: E 21 TYR cc_start: 0.7629 (m-10) cc_final: 0.7333 (m-10) REVERT: E 92 VAL cc_start: 0.7549 (OUTLIER) cc_final: 0.7224 (p) REVERT: F 89 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7283 (mt-10) REVERT: F 162 MET cc_start: 0.7572 (mtt) cc_final: 0.7162 (mtt) outliers start: 60 outliers final: 52 residues processed: 209 average time/residue: 0.2255 time to fit residues: 71.9003 Evaluate side-chains 214 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 139 HIS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 51 CYS Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 5 TRP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 62 ARG Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 202 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 24 optimal weight: 0.0870 chunk 45 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.192911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.133799 restraints weight = 56640.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.135580 restraints weight = 31046.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.137175 restraints weight = 22173.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.140000 restraints weight = 20927.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.139694 restraints weight = 18032.284| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 13870 Z= 0.256 Angle : 0.629 6.832 19272 Z= 0.357 Chirality : 0.046 0.175 2140 Planarity : 0.005 0.079 2095 Dihedral : 23.553 160.701 2739 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 6.21 % Allowed : 24.94 % Favored : 68.85 % 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: -0.58 (0.23), residues: 1347 helix: 1.38 (0.30), residues: 288 sheet: -1.53 (0.31), residues: 270 loop : -0.57 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 152 TYR 0.019 0.002 TYR B 110 PHE 0.019 0.002 PHE B 140 TRP 0.018 0.002 TRP F 5 HIS 0.008 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00580 (13864) covalent geometry : angle 0.62687 (19260) SS BOND : bond 0.00231 ( 6) SS BOND : angle 2.35932 ( 12) hydrogen bonds : bond 0.05356 ( 541) hydrogen bonds : angle 5.72261 ( 1334) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 157 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8352 (t80) cc_final: 0.7788 (t80) REVERT: A 217 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8549 (mm-30) REVERT: C 143 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7588 (ptt90) REVERT: D 159 ARG cc_start: 0.5330 (OUTLIER) cc_final: 0.4680 (pmt-80) REVERT: E 21 TYR cc_start: 0.7645 (m-10) cc_final: 0.7266 (m-10) REVERT: E 92 VAL cc_start: 0.7686 (OUTLIER) cc_final: 0.7386 (p) REVERT: F 89 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7334 (mt-10) REVERT: F 162 MET cc_start: 0.7610 (mtt) cc_final: 0.7138 (mtt) outliers start: 74 outliers final: 57 residues processed: 211 average time/residue: 0.2470 time to fit residues: 77.3110 Evaluate side-chains 214 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 153 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TRP Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 139 HIS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 51 CYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 5 TRP Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 202 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 131 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 0.1980 chunk 138 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.193518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.127439 restraints weight = 56555.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.133820 restraints weight = 30550.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.138505 restraints weight = 21282.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.141377 restraints weight = 16883.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.143579 restraints weight = 14596.123| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13870 Z= 0.220 Angle : 0.611 5.930 19272 Z= 0.346 Chirality : 0.045 0.165 2140 Planarity : 0.005 0.075 2095 Dihedral : 23.557 160.634 2739 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.88 % Allowed : 25.44 % Favored : 68.68 % 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: -0.56 (0.23), residues: 1347 helix: 1.44 (0.30), residues: 288 sheet: -1.53 (0.32), residues: 265 loop : -0.59 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 152 TYR 0.018 0.002 TYR B 110 PHE 0.016 0.002 PHE F 140 TRP 0.017 0.002 TRP F 5 HIS 0.007 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00497 (13864) covalent geometry : angle 0.60838 (19260) SS BOND : bond 0.00292 ( 6) SS BOND : angle 2.46090 ( 12) hydrogen bonds : bond 0.05096 ( 541) hydrogen bonds : angle 5.63019 ( 1334) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 157 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8360 (t80) cc_final: 0.7868 (t80) REVERT: A 217 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8341 (mm-30) REVERT: C 143 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7460 (ptt90) REVERT: D 159 ARG cc_start: 0.5376 (OUTLIER) cc_final: 0.4697 (pmt-80) REVERT: E 21 TYR cc_start: 0.7602 (m-10) cc_final: 0.7209 (m-10) REVERT: E 29 ILE cc_start: 0.7971 (mp) cc_final: 0.7714 (tp) REVERT: E 92 VAL cc_start: 0.7699 (OUTLIER) cc_final: 0.7399 (p) REVERT: F 162 MET cc_start: 0.7596 (mtt) cc_final: 0.7111 (mtt) outliers start: 70 outliers final: 60 residues processed: 207 average time/residue: 0.2260 time to fit residues: 71.5965 Evaluate side-chains 217 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 153 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TRP Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 139 HIS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 160 GLU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 51 CYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 64 TYR Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 5 TRP Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 202 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.195633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.129796 restraints weight = 56463.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.136581 restraints weight = 30244.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.141456 restraints weight = 20730.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.144487 restraints weight = 16381.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.146687 restraints weight = 14087.933| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13870 Z= 0.162 Angle : 0.579 5.924 19272 Z= 0.327 Chirality : 0.043 0.154 2140 Planarity : 0.005 0.062 2095 Dihedral : 23.505 160.362 2739 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.70 % Allowed : 26.45 % Favored : 68.85 % 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: -0.44 (0.23), residues: 1347 helix: 1.59 (0.30), residues: 288 sheet: -1.46 (0.32), residues: 260 loop : -0.55 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 152 TYR 0.014 0.001 TYR B 110 PHE 0.011 0.001 PHE F 140 TRP 0.015 0.001 TRP F 5 HIS 0.005 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00363 (13864) covalent geometry : angle 0.57584 (19260) SS BOND : bond 0.00267 ( 6) SS BOND : angle 2.42372 ( 12) hydrogen bonds : bond 0.04770 ( 541) hydrogen bonds : angle 5.42344 ( 1334) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 156 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8313 (t80) cc_final: 0.7678 (t80) REVERT: A 167 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7598 (mp) REVERT: B 142 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7454 (tp) REVERT: D 159 ARG cc_start: 0.5347 (OUTLIER) cc_final: 0.4731 (pmt-80) REVERT: E 21 TYR cc_start: 0.7558 (m-10) cc_final: 0.7136 (m-10) REVERT: E 29 ILE cc_start: 0.7984 (mp) cc_final: 0.7732 (tp) REVERT: E 92 VAL cc_start: 0.7683 (OUTLIER) cc_final: 0.7373 (p) REVERT: F 162 MET cc_start: 0.7528 (mtt) cc_final: 0.7074 (mtt) outliers start: 56 outliers final: 48 residues processed: 196 average time/residue: 0.2002 time to fit residues: 60.1101 Evaluate side-chains 205 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TRP Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 139 HIS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 51 CYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 64 TYR Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 5 TRP Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 202 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.194776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.130686 restraints weight = 56647.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.137111 restraints weight = 31231.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.141728 restraints weight = 21729.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.144526 restraints weight = 17253.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.146177 restraints weight = 14934.690| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13870 Z= 0.157 Angle : 0.573 6.203 19272 Z= 0.324 Chirality : 0.043 0.154 2140 Planarity : 0.005 0.056 2095 Dihedral : 23.437 159.997 2738 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.70 % Allowed : 26.62 % Favored : 68.68 % 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: -0.37 (0.23), residues: 1347 helix: 1.70 (0.30), residues: 288 sheet: -1.43 (0.32), residues: 260 loop : -0.51 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 58 TYR 0.013 0.001 TYR B 110 PHE 0.011 0.001 PHE A 11 TRP 0.015 0.001 TRP F 5 HIS 0.005 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00354 (13864) covalent geometry : angle 0.57055 (19260) SS BOND : bond 0.00263 ( 6) SS BOND : angle 2.35623 ( 12) hydrogen bonds : bond 0.04712 ( 541) hydrogen bonds : angle 5.27659 ( 1334) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 154 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8288 (t80) cc_final: 0.7643 (t80) REVERT: A 167 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.7622 (mp) REVERT: B 142 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7452 (tp) REVERT: C 143 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7441 (ptt90) REVERT: D 159 ARG cc_start: 0.5416 (OUTLIER) cc_final: 0.4851 (pmt-80) REVERT: E 21 TYR cc_start: 0.7562 (m-10) cc_final: 0.7168 (m-10) REVERT: E 29 ILE cc_start: 0.8006 (mp) cc_final: 0.7766 (tp) REVERT: E 92 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7357 (p) REVERT: F 162 MET cc_start: 0.7476 (mtt) cc_final: 0.7069 (mtt) outliers start: 56 outliers final: 49 residues processed: 194 average time/residue: 0.2021 time to fit residues: 60.7652 Evaluate side-chains 206 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 152 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TRP Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 139 HIS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 51 CYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 5 TRP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 202 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 56 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 112 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.193779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.131083 restraints weight = 56778.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.138820 restraints weight = 31090.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.139890 restraints weight = 21436.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.141780 restraints weight = 18876.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.142373 restraints weight = 16345.228| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13870 Z= 0.181 Angle : 0.585 6.197 19272 Z= 0.330 Chirality : 0.044 0.159 2140 Planarity : 0.005 0.060 2095 Dihedral : 23.443 160.058 2738 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 4.62 % Allowed : 26.36 % Favored : 69.02 % 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: -0.40 (0.23), residues: 1347 helix: 1.69 (0.30), residues: 288 sheet: -1.45 (0.32), residues: 259 loop : -0.54 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 58 TYR 0.014 0.001 TYR B 110 PHE 0.013 0.001 PHE F 140 TRP 0.016 0.001 TRP F 5 HIS 0.006 0.001 HIS C 27 Details of bonding type rmsd covalent geometry : bond 0.00410 (13864) covalent geometry : angle 0.58185 (19260) SS BOND : bond 0.00250 ( 6) SS BOND : angle 2.38091 ( 12) hydrogen bonds : bond 0.04818 ( 541) hydrogen bonds : angle 5.32057 ( 1334) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 152 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8300 (t80) cc_final: 0.7775 (t80) REVERT: A 167 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.7685 (mp) REVERT: C 143 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7642 (ptt90) REVERT: D 159 ARG cc_start: 0.5411 (OUTLIER) cc_final: 0.4779 (pmt-80) REVERT: D 183 GLN cc_start: 0.5823 (tm-30) cc_final: 0.5277 (tm-30) REVERT: E 11 PHE cc_start: 0.4690 (t80) cc_final: 0.4436 (t80) REVERT: E 21 TYR cc_start: 0.7638 (m-10) cc_final: 0.7219 (m-10) REVERT: E 29 ILE cc_start: 0.8021 (mp) cc_final: 0.7790 (tp) REVERT: E 92 VAL cc_start: 0.7619 (OUTLIER) cc_final: 0.7242 (p) REVERT: F 71 MET cc_start: 0.6067 (mmm) cc_final: 0.5804 (mmm) REVERT: F 162 MET cc_start: 0.7534 (mtt) cc_final: 0.7107 (mtt) outliers start: 55 outliers final: 50 residues processed: 192 average time/residue: 0.2002 time to fit residues: 59.6216 Evaluate side-chains 206 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 152 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TRP Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 212 HIS Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 139 HIS Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 51 CYS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 HIS Chi-restraints excluded: chain D residue 159 ARG Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 5 TRP Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 202 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 18 optimal weight: 0.0970 chunk 9 optimal weight: 0.0010 chunk 141 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.197219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.133718 restraints weight = 56432.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.140427 restraints weight = 30792.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.145100 restraints weight = 21360.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.148256 restraints weight = 16975.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.149969 restraints weight = 14605.074| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13870 Z= 0.131 Angle : 0.563 6.363 19272 Z= 0.316 Chirality : 0.043 0.143 2140 Planarity : 0.004 0.049 2095 Dihedral : 23.356 159.111 2738 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.03 % Allowed : 27.20 % Favored : 68.77 % 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: -0.22 (0.23), residues: 1347 helix: 1.84 (0.31), residues: 288 sheet: -1.28 (0.31), residues: 280 loop : -0.42 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 58 TYR 0.011 0.001 TYR B 110 PHE 0.009 0.001 PHE B 140 TRP 0.013 0.001 TRP D 5 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00294 (13864) covalent geometry : angle 0.56022 (19260) SS BOND : bond 0.00291 ( 6) SS BOND : angle 2.33045 ( 12) hydrogen bonds : bond 0.04532 ( 541) hydrogen bonds : angle 5.06854 ( 1334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5041.11 seconds wall clock time: 86 minutes 34.87 seconds (5194.87 seconds total)