Starting phenix.real_space_refine on Mon Jul 28 08:51:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ykm_10828/07_2025/6ykm_10828.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ykm_10828/07_2025/6ykm_10828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ykm_10828/07_2025/6ykm_10828.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ykm_10828/07_2025/6ykm_10828.map" model { file = "/net/cci-nas-00/data/ceres_data/6ykm_10828/07_2025/6ykm_10828.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ykm_10828/07_2025/6ykm_10828.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6752 2.51 5 N 1688 2.21 5 O 1924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10434 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "B" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "C" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "D" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "E" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1954 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "F" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 328 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "G" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 328 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.63, per 1000 atoms: 0.64 Number of scatterers: 10434 At special positions: 0 Unit cell: (95.68, 114.816, 99.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1924 8.00 N 1688 7.00 C 6752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.3 seconds 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2514 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 0 sheets defined 83.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 removed outlier: 3.647A pdb=" N MET A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 47 removed outlier: 3.919A pdb=" N ILE A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.656A pdb=" N LYS A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 73 through 91 Processing helix chain 'A' and resid 93 through 100 Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.662A pdb=" N ASP A 117 " --> pdb=" O MET A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 160 removed outlier: 4.062A pdb=" N GLU A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A 136 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Proline residue: A 154 - end of helix removed outlier: 3.902A pdb=" N LEU A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 174 through 199 removed outlier: 4.435A pdb=" N ALA A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 229 removed outlier: 3.886A pdb=" N ASP A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 214 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 242 Processing helix chain 'B' and resid 6 through 17 removed outlier: 3.640A pdb=" N ALA B 12 " --> pdb=" O GLY B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 32 through 47 removed outlier: 3.532A pdb=" N VAL B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Proline residue: B 41 - end of helix Processing helix chain 'B' and resid 52 through 62 removed outlier: 3.704A pdb=" N LYS B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.584A pdb=" N PHE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 91 Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.629A pdb=" N LEU B 96 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.929A pdb=" N GLU B 102 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 103 " --> pdb=" O THR B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 103' Processing helix chain 'B' and resid 105 through 113 Processing helix chain 'B' and resid 120 through 129 removed outlier: 4.031A pdb=" N GLU B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 152 removed outlier: 3.611A pdb=" N GLU B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 143 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP B 146 " --> pdb=" O CYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 174 through 198 removed outlier: 3.691A pdb=" N MET B 178 " --> pdb=" O ASN B 174 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE B 182 " --> pdb=" O MET B 178 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 198 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 229 removed outlier: 4.150A pdb=" N ASP B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU B 214 " --> pdb=" O ASN B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.518A pdb=" N ALA B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 17 removed outlier: 3.769A pdb=" N LEU C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.656A pdb=" N LEU C 22 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 47 removed outlier: 3.599A pdb=" N ILE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Proline residue: C 41 - end of helix Processing helix chain 'C' and resid 52 through 62 removed outlier: 3.543A pdb=" N LYS C 57 " --> pdb=" O LYS C 53 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.554A pdb=" N PHE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 91 removed outlier: 3.646A pdb=" N GLN C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 87 " --> pdb=" O GLU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 removed outlier: 3.736A pdb=" N LEU C 96 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU C 97 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER C 98 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR C 100 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 removed outlier: 3.623A pdb=" N MET C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP C 117 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 129 removed outlier: 3.883A pdb=" N GLU C 126 " --> pdb=" O GLU C 122 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 137 through 150 removed outlier: 3.988A pdb=" N TRP C 146 " --> pdb=" O CYS C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 164 Processing helix chain 'C' and resid 164 through 171 Processing helix chain 'C' and resid 174 through 199 removed outlier: 3.679A pdb=" N THR C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA C 188 " --> pdb=" O GLY C 184 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 199 " --> pdb=" O GLY C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 229 removed outlier: 4.161A pdb=" N ASP C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU C 214 " --> pdb=" O ASN C 210 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'D' and resid 2 through 22 removed outlier: 3.855A pdb=" N MET D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR D 14 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 22 " --> pdb=" O VAL D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 removed outlier: 3.568A pdb=" N VAL D 30 " --> pdb=" O PRO D 27 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE D 31 " --> pdb=" O LEU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 38 Processing helix chain 'D' and resid 39 through 47 Processing helix chain 'D' and resid 52 through 62 removed outlier: 3.597A pdb=" N LYS D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.631A pdb=" N PHE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 91 Processing helix chain 'D' and resid 96 through 100 removed outlier: 3.624A pdb=" N THR D 100 " --> pdb=" O GLU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 Processing helix chain 'D' and resid 120 through 163 removed outlier: 3.784A pdb=" N GLU D 126 " --> pdb=" O GLU D 122 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR D 132 " --> pdb=" O MET D 128 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN D 134 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TRP D 146 " --> pdb=" O CYS D 142 " (cutoff:3.500A) Proline residue: D 154 - end of helix removed outlier: 3.628A pdb=" N LEU D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 171 removed outlier: 3.588A pdb=" N LYS D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 199 removed outlier: 3.883A pdb=" N ALA D 180 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA D 188 " --> pdb=" O GLY D 184 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 190 " --> pdb=" O PHE D 186 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 231 removed outlier: 4.080A pdb=" N ASP D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU D 214 " --> pdb=" O ASN D 210 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'E' and resid 2 through 22 removed outlier: 3.519A pdb=" N ILE E 6 " --> pdb=" O ASP E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 3.808A pdb=" N ILE E 38 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) Proline residue: E 41 - end of helix Processing helix chain 'E' and resid 52 through 62 removed outlier: 3.532A pdb=" N LYS E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR E 60 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS E 61 " --> pdb=" O LYS E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.615A pdb=" N PHE E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 91 removed outlier: 3.781A pdb=" N GLN E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG E 89 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 95 Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.752A pdb=" N ASN E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 120 through 133 removed outlier: 4.239A pdb=" N GLU E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER E 127 " --> pdb=" O GLU E 123 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE E 130 " --> pdb=" O GLU E 126 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN E 131 " --> pdb=" O SER E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 143 Processing helix chain 'E' and resid 143 through 152 Processing helix chain 'E' and resid 152 through 171 removed outlier: 3.587A pdb=" N MET E 156 " --> pdb=" O THR E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 185 through 197 Processing helix chain 'E' and resid 199 through 229 removed outlier: 3.972A pdb=" N ASP E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU E 214 " --> pdb=" O ASN E 210 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 216 " --> pdb=" O MET E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 233 through 242 Processing helix chain 'E' and resid 243 through 245 No H-bonds generated for 'chain 'E' and resid 243 through 245' Processing helix chain 'F' and resid 16 through 39 removed outlier: 3.850A pdb=" N TYR F 20 " --> pdb=" O TRP F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 53 removed outlier: 3.974A pdb=" N GLU F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 37 Processing helix chain 'G' and resid 43 through 53 removed outlier: 3.833A pdb=" N ALA G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU G 48 " --> pdb=" O LYS G 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS G 49 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLU G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1977 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2475 1.33 - 1.45: 1955 1.45 - 1.57: 6064 1.57 - 1.69: 0 1.69 - 1.81: 125 Bond restraints: 10619 Sorted by residual: bond pdb=" C MET E 40 " pdb=" N PRO E 41 " ideal model delta sigma weight residual 1.336 1.377 -0.041 1.23e-02 6.61e+03 1.11e+01 bond pdb=" C MET B 40 " pdb=" N PRO B 41 " ideal model delta sigma weight residual 1.336 1.372 -0.037 1.23e-02 6.61e+03 8.97e+00 bond pdb=" C MET D 40 " pdb=" N PRO D 41 " ideal model delta sigma weight residual 1.336 1.372 -0.036 1.23e-02 6.61e+03 8.79e+00 bond pdb=" CG1 ILE A 78 " pdb=" CD1 ILE A 78 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.84e+00 bond pdb=" C VAL F 18 " pdb=" N PRO F 19 " ideal model delta sigma weight residual 1.335 1.362 -0.026 1.36e-02 5.41e+03 3.71e+00 ... (remaining 10614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 13668 2.17 - 4.34: 559 4.34 - 6.50: 83 6.50 - 8.67: 35 8.67 - 10.84: 3 Bond angle restraints: 14348 Sorted by residual: angle pdb=" C SER G 38 " pdb=" N LYS G 39 " pdb=" CA LYS G 39 " ideal model delta sigma weight residual 122.07 127.75 -5.68 1.43e+00 4.89e-01 1.58e+01 angle pdb=" C ALA F 43 " pdb=" N LYS F 44 " pdb=" CA LYS F 44 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C SER C 253 " pdb=" N GLN C 254 " pdb=" CA GLN C 254 " ideal model delta sigma weight residual 121.54 128.00 -6.46 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C LEU E 96 " pdb=" N GLU E 97 " pdb=" CA GLU E 97 " ideal model delta sigma weight residual 120.28 124.79 -4.51 1.34e+00 5.57e-01 1.13e+01 angle pdb=" CA LEU B 115 " pdb=" CB LEU B 115 " pdb=" CG LEU B 115 " ideal model delta sigma weight residual 116.30 127.14 -10.84 3.50e+00 8.16e-02 9.59e+00 ... (remaining 14343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 5842 14.14 - 28.28: 401 28.28 - 42.42: 112 42.42 - 56.56: 18 56.56 - 70.70: 3 Dihedral angle restraints: 6376 sinusoidal: 2490 harmonic: 3886 Sorted by residual: dihedral pdb=" CA LEU B 199 " pdb=" C LEU B 199 " pdb=" N PHE B 200 " pdb=" CA PHE B 200 " ideal model delta harmonic sigma weight residual -180.00 -153.27 -26.73 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA LEU E 199 " pdb=" C LEU E 199 " pdb=" N PHE E 200 " pdb=" CA PHE E 200 " ideal model delta harmonic sigma weight residual -180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA LEU C 199 " pdb=" C LEU C 199 " pdb=" N PHE C 200 " pdb=" CA PHE C 200 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 6373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 934 0.047 - 0.094: 550 0.094 - 0.142: 162 0.142 - 0.189: 29 0.189 - 0.236: 7 Chirality restraints: 1682 Sorted by residual: chirality pdb=" CG LEU C 158 " pdb=" CB LEU C 158 " pdb=" CD1 LEU C 158 " pdb=" CD2 LEU C 158 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE E 182 " pdb=" CA ILE E 182 " pdb=" CG1 ILE E 182 " pdb=" CG2 ILE E 182 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CG LEU G 28 " pdb=" CB LEU G 28 " pdb=" CD1 LEU G 28 " pdb=" CD2 LEU G 28 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1679 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 149 " -0.028 2.00e-02 2.50e+03 3.07e-02 1.65e+01 pdb=" CG PHE E 149 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE E 149 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE E 149 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE E 149 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE E 149 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE E 149 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 149 " 0.030 2.00e-02 2.50e+03 3.06e-02 1.64e+01 pdb=" CG PHE C 149 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE C 149 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE C 149 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 149 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE C 149 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 149 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 149 " 0.029 2.00e-02 2.50e+03 2.95e-02 1.52e+01 pdb=" CG PHE B 149 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 PHE B 149 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE B 149 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 149 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 149 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 149 " 0.011 2.00e-02 2.50e+03 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2487 2.78 - 3.31: 10069 3.31 - 3.84: 17573 3.84 - 4.37: 22131 4.37 - 4.90: 36677 Nonbonded interactions: 88937 Sorted by model distance: nonbonded pdb=" O ILE C 38 " pdb=" OG1 THR C 42 " model vdw 2.256 3.040 nonbonded pdb=" OE2 GLU A 23 " pdb=" OG SER B 34 " model vdw 2.304 3.040 nonbonded pdb=" O HOH B 303 " pdb=" O HOH F 304 " model vdw 2.327 3.040 nonbonded pdb=" OG SER F 25 " pdb=" O HOH F 301 " model vdw 2.343 3.040 nonbonded pdb=" OE2 GLU C 23 " pdb=" OG SER D 34 " model vdw 2.370 3.040 ... (remaining 88932 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.600 Find NCS groups from input model: 0.380 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.009 0.095 10619 Z= 0.367 Angle : 1.067 10.840 14348 Z= 0.565 Chirality : 0.061 0.236 1682 Planarity : 0.008 0.062 1804 Dihedral : 11.095 70.703 3862 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.68 (0.17), residues: 1343 helix: -3.20 (0.11), residues: 1092 sheet: None (None), residues: 0 loop : -1.13 (0.33), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP F 35 HIS 0.010 0.002 HIS B 52 PHE 0.068 0.005 PHE C 149 TYR 0.045 0.005 TYR C 197 ARG 0.008 0.001 ARG D 251 Details of bonding type rmsd hydrogen bonds : bond 0.15615 ( 671) hydrogen bonds : angle 7.44956 ( 1977) covalent geometry : bond 0.00908 (10619) covalent geometry : angle 1.06670 (14348) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.190 Fit side-chains REVERT: A 208 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7929 (tttm) REVERT: B 110 ASN cc_start: 0.8038 (p0) cc_final: 0.7680 (m110) REVERT: B 140 LYS cc_start: 0.8163 (ttmp) cc_final: 0.7759 (mtmm) REVERT: B 226 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8303 (ttmm) REVERT: C 40 MET cc_start: 0.8113 (mmt) cc_final: 0.7727 (mmt) REVERT: C 216 LYS cc_start: 0.8497 (tptm) cc_final: 0.7735 (mttt) REVERT: D 151 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7041 (mt-10) REVERT: D 223 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7763 (mm-30) REVERT: D 230 GLU cc_start: 0.7084 (mp0) cc_final: 0.6849 (mt-10) REVERT: E 28 LEU cc_start: 0.7127 (tt) cc_final: 0.6687 (mp) REVERT: E 61 LYS cc_start: 0.8339 (mttp) cc_final: 0.8068 (mtmt) REVERT: E 104 GLU cc_start: 0.7561 (mp0) cc_final: 0.7230 (mm-30) REVERT: E 140 LYS cc_start: 0.8461 (ptpt) cc_final: 0.8012 (pttm) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2622 time to fit residues: 95.9365 Evaluate side-chains 186 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 138 HIS C 52 HIS C 134 GLN D 110 ASN D 134 GLN E 134 GLN E 138 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.146052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.116386 restraints weight = 11526.144| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.57 r_work: 0.3005 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10619 Z= 0.136 Angle : 0.580 6.845 14348 Z= 0.300 Chirality : 0.041 0.144 1682 Planarity : 0.005 0.047 1804 Dihedral : 5.273 22.929 1402 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.26 % Allowed : 7.94 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.21), residues: 1343 helix: -1.64 (0.14), residues: 1093 sheet: None (None), residues: 0 loop : -0.56 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 35 HIS 0.009 0.001 HIS E 138 PHE 0.023 0.002 PHE B 149 TYR 0.020 0.002 TYR C 197 ARG 0.004 0.001 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 671) hydrogen bonds : angle 4.56181 ( 1977) covalent geometry : bond 0.00307 (10619) covalent geometry : angle 0.58005 (14348) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 1.165 Fit side-chains REVERT: A 23 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7530 (tt0) REVERT: A 126 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8066 (mm-30) REVERT: A 172 LEU cc_start: 0.5958 (pt) cc_final: 0.5732 (pt) REVERT: A 208 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8127 (tttm) REVERT: B 54 LYS cc_start: 0.8906 (mmtm) cc_final: 0.8683 (mmmm) REVERT: B 140 LYS cc_start: 0.8534 (ttmp) cc_final: 0.8174 (mtmm) REVERT: B 226 LYS cc_start: 0.8704 (ttmt) cc_final: 0.8449 (ttmm) REVERT: C 57 LYS cc_start: 0.8693 (mtmt) cc_final: 0.8492 (mttp) REVERT: D 33 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8547 (tp) REVERT: D 133 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7609 (mm-30) REVERT: D 151 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7631 (mt-10) REVERT: E 3 LEU cc_start: 0.7562 (tp) cc_final: 0.7358 (tp) REVERT: E 28 LEU cc_start: 0.6407 (tt) cc_final: 0.5973 (mp) REVERT: E 61 LYS cc_start: 0.8640 (mttp) cc_final: 0.8318 (mtmt) REVERT: E 64 LYS cc_start: 0.7952 (pttm) cc_final: 0.6643 (mmmt) REVERT: E 104 GLU cc_start: 0.8264 (mp0) cc_final: 0.7573 (mm-30) REVERT: E 117 ASP cc_start: 0.8276 (m-30) cc_final: 0.8026 (m-30) REVERT: E 140 LYS cc_start: 0.8859 (ptpt) cc_final: 0.8415 (pttm) REVERT: E 151 GLU cc_start: 0.7930 (tt0) cc_final: 0.7700 (mt-10) outliers start: 25 outliers final: 11 residues processed: 216 average time/residue: 0.2698 time to fit residues: 78.6562 Evaluate side-chains 181 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 138 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 97 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 60 optimal weight: 0.0030 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 89 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 HIS D 110 ASN E 243 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.143397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.115947 restraints weight = 11675.013| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.38 r_work: 0.3047 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10619 Z= 0.109 Angle : 0.528 9.045 14348 Z= 0.268 Chirality : 0.040 0.121 1682 Planarity : 0.004 0.040 1804 Dihedral : 4.797 21.926 1402 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.17 % Allowed : 9.93 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.22), residues: 1343 helix: -0.87 (0.15), residues: 1100 sheet: None (None), residues: 0 loop : -0.25 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 203 HIS 0.014 0.001 HIS E 138 PHE 0.019 0.001 PHE A 149 TYR 0.017 0.002 TYR C 197 ARG 0.004 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 671) hydrogen bonds : angle 4.15314 ( 1977) covalent geometry : bond 0.00234 (10619) covalent geometry : angle 0.52820 (14348) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 1.248 Fit side-chains REVERT: A 23 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7507 (tt0) REVERT: A 61 LYS cc_start: 0.8340 (mtpp) cc_final: 0.7529 (mmtt) REVERT: A 172 LEU cc_start: 0.5826 (pt) cc_final: 0.5574 (pt) REVERT: B 54 LYS cc_start: 0.8905 (mmtm) cc_final: 0.8659 (mmmm) REVERT: B 110 ASN cc_start: 0.8191 (m-40) cc_final: 0.7866 (m110) REVERT: B 113 MET cc_start: 0.8407 (ptm) cc_final: 0.8080 (ptp) REVERT: B 140 LYS cc_start: 0.8424 (ttmp) cc_final: 0.7987 (mtmm) REVERT: B 226 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8413 (ttmm) REVERT: C 61 LYS cc_start: 0.8389 (mmtt) cc_final: 0.7944 (ttpp) REVERT: D 33 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8383 (tp) REVERT: D 133 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7503 (mm-30) REVERT: D 151 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7548 (mt-10) REVERT: E 9 MET cc_start: 0.7818 (mtp) cc_final: 0.7597 (mtm) REVERT: E 64 LYS cc_start: 0.7973 (pttm) cc_final: 0.6582 (mmmt) REVERT: E 104 GLU cc_start: 0.8197 (mp0) cc_final: 0.7534 (mm-30) REVERT: E 117 ASP cc_start: 0.8202 (m-30) cc_final: 0.7925 (m-30) REVERT: E 140 LYS cc_start: 0.8717 (ptpt) cc_final: 0.8305 (ptmm) REVERT: E 151 GLU cc_start: 0.7898 (tt0) cc_final: 0.7654 (mt-10) REVERT: E 207 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8401 (tt) REVERT: E 208 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8080 (mtmm) outliers start: 24 outliers final: 7 residues processed: 196 average time/residue: 0.2437 time to fit residues: 65.9973 Evaluate side-chains 176 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 103 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 HIS E 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.139882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.111822 restraints weight = 11421.544| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.37 r_work: 0.2986 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10619 Z= 0.148 Angle : 0.558 7.651 14348 Z= 0.284 Chirality : 0.042 0.124 1682 Planarity : 0.004 0.039 1804 Dihedral : 4.748 21.602 1402 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.62 % Allowed : 11.37 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.22), residues: 1343 helix: -0.52 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : -0.11 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 146 HIS 0.004 0.001 HIS D 138 PHE 0.023 0.002 PHE B 149 TYR 0.027 0.002 TYR D 197 ARG 0.005 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 671) hydrogen bonds : angle 4.10295 ( 1977) covalent geometry : bond 0.00354 (10619) covalent geometry : angle 0.55831 (14348) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 1.170 Fit side-chains REVERT: A 23 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7504 (tt0) REVERT: B 54 LYS cc_start: 0.8920 (mmtm) cc_final: 0.8700 (mmmm) REVERT: B 110 ASN cc_start: 0.8282 (m-40) cc_final: 0.8019 (m-40) REVERT: B 113 MET cc_start: 0.8332 (ptm) cc_final: 0.8026 (ptp) REVERT: B 140 LYS cc_start: 0.8497 (ttmp) cc_final: 0.8012 (mtmm) REVERT: B 178 MET cc_start: 0.7137 (tpt) cc_final: 0.6639 (tpt) REVERT: B 226 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8491 (ttpp) REVERT: D 33 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8445 (tp) REVERT: D 38 ILE cc_start: 0.8724 (tt) cc_final: 0.8417 (tt) REVERT: D 133 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7608 (mm-30) REVERT: D 151 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7591 (mt-10) REVERT: E 9 MET cc_start: 0.7906 (mtp) cc_final: 0.7658 (mtm) REVERT: E 64 LYS cc_start: 0.8015 (pttm) cc_final: 0.6594 (mmmt) REVERT: E 104 GLU cc_start: 0.8253 (mp0) cc_final: 0.7627 (mm-30) REVERT: E 117 ASP cc_start: 0.8228 (m-30) cc_final: 0.7985 (m-30) REVERT: E 140 LYS cc_start: 0.8676 (ptpt) cc_final: 0.8231 (mtmm) REVERT: E 151 GLU cc_start: 0.7846 (tt0) cc_final: 0.7625 (mt-10) REVERT: E 207 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8351 (tt) outliers start: 18 outliers final: 10 residues processed: 182 average time/residue: 0.2489 time to fit residues: 62.8537 Evaluate side-chains 176 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 111 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.140508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.112751 restraints weight = 11539.651| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.34 r_work: 0.2994 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10619 Z= 0.131 Angle : 0.527 7.019 14348 Z= 0.270 Chirality : 0.040 0.118 1682 Planarity : 0.004 0.038 1804 Dihedral : 4.615 21.121 1402 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.71 % Allowed : 12.36 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.23), residues: 1343 helix: -0.22 (0.15), residues: 1106 sheet: None (None), residues: 0 loop : 0.18 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 16 HIS 0.003 0.001 HIS B 52 PHE 0.019 0.001 PHE B 149 TYR 0.019 0.002 TYR D 197 ARG 0.007 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 671) hydrogen bonds : angle 3.99151 ( 1977) covalent geometry : bond 0.00307 (10619) covalent geometry : angle 0.52702 (14348) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.211 Fit side-chains REVERT: B 54 LYS cc_start: 0.8950 (mmtm) cc_final: 0.8690 (mmmm) REVERT: B 110 ASN cc_start: 0.8396 (m-40) cc_final: 0.8168 (m-40) REVERT: B 113 MET cc_start: 0.8288 (ptm) cc_final: 0.7960 (ptp) REVERT: B 140 LYS cc_start: 0.8480 (ttmp) cc_final: 0.7984 (mtmm) REVERT: B 226 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8462 (ttpp) REVERT: D 33 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8455 (tp) REVERT: D 38 ILE cc_start: 0.8746 (tt) cc_final: 0.8496 (tt) REVERT: D 133 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7582 (mm-30) REVERT: E 9 MET cc_start: 0.7962 (mtp) cc_final: 0.7716 (mtm) REVERT: E 64 LYS cc_start: 0.7952 (pttm) cc_final: 0.6568 (mmmt) REVERT: E 104 GLU cc_start: 0.8218 (mp0) cc_final: 0.7581 (mm-30) REVERT: E 117 ASP cc_start: 0.8162 (m-30) cc_final: 0.7929 (m-30) REVERT: E 140 LYS cc_start: 0.8674 (ptpt) cc_final: 0.8057 (mttt) REVERT: E 207 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8361 (tt) outliers start: 19 outliers final: 14 residues processed: 170 average time/residue: 0.2435 time to fit residues: 57.5837 Evaluate side-chains 174 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.140775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.112888 restraints weight = 11603.850| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.44 r_work: 0.2994 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10619 Z= 0.130 Angle : 0.523 6.814 14348 Z= 0.268 Chirality : 0.041 0.118 1682 Planarity : 0.004 0.037 1804 Dihedral : 4.554 20.941 1402 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.99 % Allowed : 13.09 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.23), residues: 1343 helix: 0.00 (0.16), residues: 1106 sheet: None (None), residues: 0 loop : 0.40 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 16 HIS 0.003 0.001 HIS A 138 PHE 0.019 0.001 PHE B 149 TYR 0.018 0.002 TYR D 197 ARG 0.008 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 671) hydrogen bonds : angle 3.95789 ( 1977) covalent geometry : bond 0.00307 (10619) covalent geometry : angle 0.52253 (14348) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 1.164 Fit side-chains REVERT: B 54 LYS cc_start: 0.8951 (mmtm) cc_final: 0.8696 (mmmm) REVERT: B 110 ASN cc_start: 0.8375 (m-40) cc_final: 0.8137 (m-40) REVERT: B 113 MET cc_start: 0.8249 (ptm) cc_final: 0.7937 (ptp) REVERT: B 140 LYS cc_start: 0.8467 (ttmp) cc_final: 0.7972 (mtmm) REVERT: B 151 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7960 (mt-10) REVERT: B 167 LEU cc_start: 0.8878 (tm) cc_final: 0.8605 (tp) REVERT: C 112 MET cc_start: 0.8513 (mmm) cc_final: 0.8303 (mmm) REVERT: D 33 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8509 (tp) REVERT: D 38 ILE cc_start: 0.8764 (tt) cc_final: 0.8518 (tt) REVERT: D 133 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7637 (mm-30) REVERT: D 151 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7682 (mt-10) REVERT: E 1 MET cc_start: 0.7006 (tpp) cc_final: 0.6788 (tpp) REVERT: E 9 MET cc_start: 0.7975 (mtp) cc_final: 0.7729 (mtm) REVERT: E 64 LYS cc_start: 0.7987 (pttm) cc_final: 0.6625 (mmmt) REVERT: E 104 GLU cc_start: 0.8238 (mp0) cc_final: 0.7612 (mm-30) REVERT: E 113 MET cc_start: 0.8490 (ttp) cc_final: 0.8156 (mtp) REVERT: E 117 ASP cc_start: 0.8172 (m-30) cc_final: 0.7959 (m-30) REVERT: E 140 LYS cc_start: 0.8672 (ptpt) cc_final: 0.8090 (mttt) REVERT: E 207 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8393 (tt) outliers start: 22 outliers final: 15 residues processed: 177 average time/residue: 0.2344 time to fit residues: 58.1707 Evaluate side-chains 174 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 1 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 123 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.141092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.114110 restraints weight = 11649.992| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.35 r_work: 0.2979 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10619 Z= 0.153 Angle : 0.539 7.033 14348 Z= 0.277 Chirality : 0.042 0.177 1682 Planarity : 0.004 0.037 1804 Dihedral : 4.608 21.475 1402 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.08 % Allowed : 13.18 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.23), residues: 1343 helix: 0.15 (0.16), residues: 1085 sheet: None (None), residues: 0 loop : 0.61 (0.43), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 16 HIS 0.004 0.001 HIS D 52 PHE 0.020 0.002 PHE B 149 TYR 0.018 0.002 TYR D 197 ARG 0.009 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 671) hydrogen bonds : angle 4.00249 ( 1977) covalent geometry : bond 0.00371 (10619) covalent geometry : angle 0.53906 (14348) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 1.173 Fit side-chains REVERT: B 54 LYS cc_start: 0.8941 (mmtm) cc_final: 0.8694 (mmmm) REVERT: B 110 ASN cc_start: 0.8422 (m-40) cc_final: 0.8135 (m-40) REVERT: B 113 MET cc_start: 0.8234 (ptm) cc_final: 0.7948 (ptp) REVERT: B 140 LYS cc_start: 0.8507 (ttmp) cc_final: 0.7971 (mtmm) REVERT: B 151 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8002 (mt-10) REVERT: D 33 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8553 (tp) REVERT: D 38 ILE cc_start: 0.8796 (tt) cc_final: 0.8527 (tt) REVERT: D 133 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7580 (mm-30) REVERT: D 151 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7638 (mt-10) REVERT: E 1 MET cc_start: 0.6916 (tpp) cc_final: 0.6690 (tpp) REVERT: E 9 MET cc_start: 0.7957 (mtp) cc_final: 0.7692 (mtm) REVERT: E 64 LYS cc_start: 0.7991 (pttm) cc_final: 0.6611 (mmmt) REVERT: E 104 GLU cc_start: 0.8227 (mp0) cc_final: 0.7628 (mm-30) REVERT: E 113 MET cc_start: 0.8484 (ttp) cc_final: 0.8176 (mtp) REVERT: E 140 LYS cc_start: 0.8632 (ptpt) cc_final: 0.8035 (mttt) REVERT: E 207 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8356 (tt) outliers start: 23 outliers final: 17 residues processed: 178 average time/residue: 0.2268 time to fit residues: 56.7398 Evaluate side-chains 184 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 27 optimal weight: 0.0770 chunk 30 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.140710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.112844 restraints weight = 11514.154| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.35 r_work: 0.2995 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10619 Z= 0.118 Angle : 0.513 6.586 14348 Z= 0.262 Chirality : 0.040 0.173 1682 Planarity : 0.004 0.037 1804 Dihedral : 4.471 20.859 1402 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.90 % Allowed : 13.54 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.23), residues: 1343 helix: 0.37 (0.16), residues: 1091 sheet: None (None), residues: 0 loop : 0.75 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 203 HIS 0.003 0.001 HIS D 52 PHE 0.015 0.001 PHE B 149 TYR 0.015 0.002 TYR D 197 ARG 0.008 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 671) hydrogen bonds : angle 3.89208 ( 1977) covalent geometry : bond 0.00273 (10619) covalent geometry : angle 0.51255 (14348) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 1.193 Fit side-chains REVERT: B 54 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8691 (mmmm) REVERT: B 113 MET cc_start: 0.8217 (ptm) cc_final: 0.7987 (ptp) REVERT: B 132 THR cc_start: 0.9248 (t) cc_final: 0.9028 (m) REVERT: B 140 LYS cc_start: 0.8477 (ttmp) cc_final: 0.8005 (mtmm) REVERT: B 151 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8017 (mt-10) REVERT: B 207 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8661 (tt) REVERT: C 112 MET cc_start: 0.8534 (mmm) cc_final: 0.8301 (mmm) REVERT: C 171 LEU cc_start: 0.6566 (mp) cc_final: 0.6244 (mp) REVERT: D 33 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8551 (tp) REVERT: D 38 ILE cc_start: 0.8774 (tt) cc_final: 0.8520 (tt) REVERT: D 133 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7610 (mm-30) REVERT: D 151 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7691 (mt-10) REVERT: E 1 MET cc_start: 0.6954 (tpp) cc_final: 0.6746 (tpp) REVERT: E 9 MET cc_start: 0.7944 (mtp) cc_final: 0.7680 (mtm) REVERT: E 64 LYS cc_start: 0.7910 (pttm) cc_final: 0.6536 (mmmt) REVERT: E 102 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7307 (pp20) REVERT: E 104 GLU cc_start: 0.8219 (mp0) cc_final: 0.7628 (mm-30) REVERT: E 113 MET cc_start: 0.8426 (ttp) cc_final: 0.8131 (mtp) REVERT: E 140 LYS cc_start: 0.8655 (ptpt) cc_final: 0.8101 (mttt) REVERT: E 207 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8405 (tt) outliers start: 21 outliers final: 15 residues processed: 186 average time/residue: 0.2378 time to fit residues: 61.7093 Evaluate side-chains 178 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 8 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 127 optimal weight: 0.0040 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.140818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.112838 restraints weight = 11624.067| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.35 r_work: 0.2999 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10619 Z= 0.120 Angle : 0.517 6.540 14348 Z= 0.263 Chirality : 0.040 0.152 1682 Planarity : 0.004 0.038 1804 Dihedral : 4.431 20.800 1402 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.99 % Allowed : 13.81 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.23), residues: 1343 helix: 0.48 (0.16), residues: 1091 sheet: None (None), residues: 0 loop : 0.89 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 16 HIS 0.003 0.001 HIS D 52 PHE 0.015 0.001 PHE B 149 TYR 0.015 0.002 TYR D 197 ARG 0.009 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 671) hydrogen bonds : angle 3.87389 ( 1977) covalent geometry : bond 0.00279 (10619) covalent geometry : angle 0.51715 (14348) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 1.180 Fit side-chains REVERT: B 54 LYS cc_start: 0.8940 (mmtm) cc_final: 0.8689 (mmmm) REVERT: B 132 THR cc_start: 0.9221 (t) cc_final: 0.9003 (m) REVERT: B 140 LYS cc_start: 0.8480 (ttmp) cc_final: 0.7999 (mtmm) REVERT: B 151 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8016 (mt-10) REVERT: B 207 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8660 (tt) REVERT: C 171 LEU cc_start: 0.6678 (mp) cc_final: 0.6403 (mp) REVERT: D 33 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8565 (tp) REVERT: D 38 ILE cc_start: 0.8802 (tt) cc_final: 0.8555 (tt) REVERT: D 133 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7595 (mm-30) REVERT: D 151 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7661 (mt-10) REVERT: E 1 MET cc_start: 0.6927 (tpp) cc_final: 0.6722 (tpp) REVERT: E 9 MET cc_start: 0.7949 (mtp) cc_final: 0.7675 (mtm) REVERT: E 64 LYS cc_start: 0.7889 (pttm) cc_final: 0.6515 (mmmt) REVERT: E 102 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7107 (mt-10) REVERT: E 104 GLU cc_start: 0.8255 (mp0) cc_final: 0.7602 (mm-30) REVERT: E 113 MET cc_start: 0.8457 (ttp) cc_final: 0.8170 (mtp) REVERT: E 140 LYS cc_start: 0.8617 (ptpt) cc_final: 0.8266 (mtpt) REVERT: E 207 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8422 (tt) outliers start: 22 outliers final: 16 residues processed: 180 average time/residue: 0.2323 time to fit residues: 58.7403 Evaluate side-chains 182 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.139762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.108633 restraints weight = 11558.802| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.60 r_work: 0.2979 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10619 Z= 0.136 Angle : 0.535 8.568 14348 Z= 0.270 Chirality : 0.041 0.141 1682 Planarity : 0.004 0.038 1804 Dihedral : 4.477 20.904 1402 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.90 % Allowed : 14.26 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.23), residues: 1343 helix: 0.49 (0.16), residues: 1091 sheet: None (None), residues: 0 loop : 0.91 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 16 HIS 0.004 0.001 HIS D 52 PHE 0.017 0.001 PHE B 149 TYR 0.015 0.002 TYR D 197 ARG 0.009 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 671) hydrogen bonds : angle 3.91814 ( 1977) covalent geometry : bond 0.00324 (10619) covalent geometry : angle 0.53537 (14348) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 1.112 Fit side-chains REVERT: B 54 LYS cc_start: 0.8966 (mmtm) cc_final: 0.8713 (mmmm) REVERT: B 132 THR cc_start: 0.9226 (t) cc_final: 0.8996 (m) REVERT: B 140 LYS cc_start: 0.8546 (ttmp) cc_final: 0.8057 (mtmm) REVERT: B 151 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8061 (mt-10) REVERT: B 207 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8825 (tt) REVERT: C 171 LEU cc_start: 0.6688 (mp) cc_final: 0.6369 (mp) REVERT: D 33 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8600 (tp) REVERT: D 38 ILE cc_start: 0.8818 (tt) cc_final: 0.8565 (tt) REVERT: D 133 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7653 (mm-30) REVERT: D 151 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7686 (mt-10) REVERT: E 9 MET cc_start: 0.7954 (mtp) cc_final: 0.7686 (mtm) REVERT: E 64 LYS cc_start: 0.7981 (pttm) cc_final: 0.6614 (mmmt) REVERT: E 102 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7049 (mt-10) REVERT: E 104 GLU cc_start: 0.8286 (mp0) cc_final: 0.7643 (mm-30) REVERT: E 140 LYS cc_start: 0.8664 (ptpt) cc_final: 0.8302 (mtpt) REVERT: E 207 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8443 (tt) outliers start: 21 outliers final: 15 residues processed: 184 average time/residue: 0.2240 time to fit residues: 58.0439 Evaluate side-chains 184 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 HIS Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 0.0040 chunk 61 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.141132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.113318 restraints weight = 11476.877| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.35 r_work: 0.3003 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10619 Z= 0.116 Angle : 0.516 7.198 14348 Z= 0.260 Chirality : 0.040 0.131 1682 Planarity : 0.004 0.038 1804 Dihedral : 4.379 20.563 1402 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.81 % Allowed : 14.62 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1343 helix: 0.61 (0.16), residues: 1091 sheet: None (None), residues: 0 loop : 0.97 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 203 HIS 0.003 0.001 HIS C 125 PHE 0.014 0.001 PHE B 149 TYR 0.014 0.002 TYR D 197 ARG 0.009 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 671) hydrogen bonds : angle 3.85585 ( 1977) covalent geometry : bond 0.00267 (10619) covalent geometry : angle 0.51595 (14348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5465.64 seconds wall clock time: 94 minutes 29.70 seconds (5669.70 seconds total)