Starting phenix.real_space_refine on Sun Aug 24 06:25:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tm3_41377/08_2025/8tm3_41377.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tm3_41377/08_2025/8tm3_41377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tm3_41377/08_2025/8tm3_41377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tm3_41377/08_2025/8tm3_41377.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tm3_41377/08_2025/8tm3_41377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tm3_41377/08_2025/8tm3_41377.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 95 5.16 5 C 11211 2.51 5 N 3010 2.21 5 O 3246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17562 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1653 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 10, 'TRANS': 217} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 11, 'ARG:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "B" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1731 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 233} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 10, 'GLN:plan1': 3, 'TYR:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1734 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 224} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1780 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 232} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 5, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 44 Chain: "E" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1839 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 229} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1788 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 236} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 8, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "G" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1815 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 8, 'TRANS': 232} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "c" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1777 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 11, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 7, 'GLU:plan': 7, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 87 Chain: "d" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1782 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 16, 'TRANS': 233} Chain breaks: 2 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 3, 'GLN:plan1': 4, 'ARG:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 99 Chain: "i" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 841 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "j" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 822 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 3, 'GLU:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 57 Time building chain proxies: 3.77, per 1000 atoms: 0.21 Number of scatterers: 17562 At special positions: 0 Unit cell: (128.26, 119.78, 136.74, 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 95 16.00 O 3246 8.00 N 3010 7.00 C 11211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 154 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 610.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4462 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 23 sheets defined 41.1% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 80 through 102 Processing helix chain 'A' and resid 106 through 124 Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 166 through 178 Processing helix chain 'A' and resid 186 through 198 Processing helix chain 'A' and resid 222 through 232 removed outlier: 3.532A pdb=" N TYR A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 30 Processing helix chain 'B' and resid 79 through 101 Processing helix chain 'B' and resid 106 through 124 Processing helix chain 'B' and resid 168 through 177 removed outlier: 4.183A pdb=" N VAL B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 185 through 201 Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 230 through 245 Processing helix chain 'C' and resid 16 through 28 Processing helix chain 'C' and resid 76 through 98 removed outlier: 3.607A pdb=" N ALA C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 121 Processing helix chain 'C' and resid 164 through 176 Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 184 through 199 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 221 through 237 Processing helix chain 'D' and resid 21 through 34 removed outlier: 3.501A pdb=" N GLY D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 104 removed outlier: 4.083A pdb=" N THR D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU D 88 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 122 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'E' and resid 1 through 7 removed outlier: 3.511A pdb=" N ASN E 4 " --> pdb=" O MET E 1 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP E 7 " --> pdb=" O ASN E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 3.574A pdb=" N GLU E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 29 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS E 30 " --> pdb=" O MET E 26 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 99 Processing helix chain 'E' and resid 104 through 122 removed outlier: 3.855A pdb=" N ILE E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Proline residue: E 119 - end of helix Processing helix chain 'E' and resid 165 through 175 Processing helix chain 'E' and resid 175 through 181 Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 225 through 234 removed outlier: 4.007A pdb=" N SER E 230 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Proline residue: E 231 - end of helix Processing helix chain 'F' and resid 21 through 34 removed outlier: 3.776A pdb=" N GLU F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.784A pdb=" N TYR F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 180 Processing helix chain 'F' and resid 186 through 202 removed outlier: 3.601A pdb=" N ILE F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS F 192 " --> pdb=" O ARG F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 222 No H-bonds generated for 'chain 'F' and resid 220 through 222' Processing helix chain 'F' and resid 229 through 245 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 128 Processing helix chain 'G' and resid 171 through 186 removed outlier: 3.713A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS G 186 " --> pdb=" O LYS G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 231 through 244 Processing helix chain 'c' and resid 35 through 46 Processing helix chain 'c' and resid 61 through 66 Processing helix chain 'c' and resid 76 through 87 Processing helix chain 'c' and resid 88 through 90 No H-bonds generated for 'chain 'c' and resid 88 through 90' Processing helix chain 'c' and resid 142 through 154 removed outlier: 4.540A pdb=" N TYR c 147 " --> pdb=" O GLU c 143 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLN c 148 " --> pdb=" O ASP c 144 " (cutoff:3.500A) Processing helix chain 'c' and resid 171 through 175 Processing helix chain 'c' and resid 180 through 184 Processing helix chain 'c' and resid 214 through 226 Processing helix chain 'c' and resid 243 through 251 removed outlier: 3.766A pdb=" N VAL c 247 " --> pdb=" O ASP c 243 " (cutoff:3.500A) Processing helix chain 'c' and resid 251 through 256 removed outlier: 4.083A pdb=" N SER c 255 " --> pdb=" O LYS c 251 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR c 256 " --> pdb=" O PRO c 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 251 through 256' Processing helix chain 'c' and resid 266 through 278 removed outlier: 3.543A pdb=" N LEU c 276 " --> pdb=" O ILE c 272 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET c 277 " --> pdb=" O LEU c 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 40 Processing helix chain 'd' and resid 64 through 69 removed outlier: 3.512A pdb=" N THR d 69 " --> pdb=" O GLU d 65 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 84 Processing helix chain 'd' and resid 98 through 114 Processing helix chain 'd' and resid 131 through 136 Processing helix chain 'd' and resid 148 through 159 Processing helix chain 'd' and resid 185 through 198 removed outlier: 4.117A pdb=" N THR d 189 " --> pdb=" O GLY d 185 " (cutoff:3.500A) Processing helix chain 'd' and resid 213 through 229 Processing helix chain 'i' and resid 53 through 58 removed outlier: 4.214A pdb=" N VAL i 57 " --> pdb=" O VAL i 53 " (cutoff:3.500A) Processing helix chain 'i' and resid 72 through 90 removed outlier: 5.081A pdb=" N PHE i 85 " --> pdb=" O ASN i 81 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL i 86 " --> pdb=" O LEU i 82 " (cutoff:3.500A) Processing helix chain 'i' and resid 105 through 119 Processing helix chain 'j' and resid 75 through 87 Processing helix chain 'j' and resid 102 through 119 removed outlier: 3.734A pdb=" N LEU j 106 " --> pdb=" O SER j 102 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 135 removed outlier: 3.579A pdb=" N PHE A 156 " --> pdb=" O GLN A 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 161 through 164 removed outlier: 4.276A pdb=" N ILE B 213 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.845A pdb=" N LEU B 134 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 138 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN B 149 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR B 156 " --> pdb=" O GLN B 149 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP B 151 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AA8, first strand: chain 'C' and resid 63 through 65 removed outlier: 3.524A pdb=" N VAL C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY C 135 " --> pdb=" O ARG C 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 167 through 170 Processing sheet with id=AB1, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.409A pdb=" N ILE D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU D 153 " --> pdb=" O CYS D 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.709A pdb=" N ILE E 212 " --> pdb=" O TYR E 224 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 63 through 65 removed outlier: 3.857A pdb=" N SER E 73 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU E 133 " --> pdb=" O SER E 73 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE E 144 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 76 through 77 Processing sheet with id=AB5, first strand: chain 'F' and resid 163 through 166 Processing sheet with id=AB6, first strand: chain 'F' and resid 67 through 69 removed outlier: 3.981A pdb=" N GLY F 139 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA F 77 " --> pdb=" O MET F 137 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE F 136 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR F 159 " --> pdb=" O MET F 151 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP F 153 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL F 157 " --> pdb=" O ASP F 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.903A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL G 217 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 69 through 73 removed outlier: 6.595A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'c' and resid 48 through 51 removed outlier: 5.447A pdb=" N GLU c 95 " --> pdb=" O HIS c 125 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N HIS c 125 " --> pdb=" O GLU c 95 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY c 97 " --> pdb=" O PHE c 123 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N CYS c 121 " --> pdb=" O ALA c 99 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LYS c 70 " --> pdb=" O PHE c 133 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N CYS c 135 " --> pdb=" O LYS c 70 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE c 72 " --> pdb=" O CYS c 135 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N CYS c 137 " --> pdb=" O ILE c 72 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ALA c 74 " --> pdb=" O CYS c 137 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N CYS c 169 " --> pdb=" O ILE c 75 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE c 164 " --> pdb=" O ILE c 231 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR c 233 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE c 166 " --> pdb=" O TYR c 233 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N CYS c 235 " --> pdb=" O ILE c 166 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N THR c 168 " --> pdb=" O CYS c 235 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 211 through 213 Processing sheet with id=AC2, first strand: chain 'd' and resid 2 through 4 removed outlier: 7.396A pdb=" N VAL d 77 " --> pdb=" O ILE d 44 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TYR d 46 " --> pdb=" O ALA d 75 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ALA d 75 " --> pdb=" O TYR d 46 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU d 76 " --> pdb=" O GLN d 89 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 16 through 20 removed outlier: 6.752A pdb=" N LEU d 17 " --> pdb=" O ILE d 119 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU d 121 " --> pdb=" O LEU d 17 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N MET d 19 " --> pdb=" O LEU d 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'i' and resid 8 through 16 removed outlier: 4.196A pdb=" N ILE i 8 " --> pdb=" O ALA i 27 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR i 37 " --> pdb=" O GLN i 22 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU i 45 " --> pdb=" O LEU i 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'j' and resid 17 through 18 removed outlier: 3.513A pdb=" N PHE j 17 " --> pdb=" O PHE j 28 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU j 37 " --> pdb=" O PHE j 92 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N SER j 94 " --> pdb=" O LEU j 37 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU j 39 " --> pdb=" O SER j 94 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU j 68 " --> pdb=" O LEU j 50 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL j 52 " --> pdb=" O SER j 66 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N SER j 66 " --> pdb=" O VAL j 52 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N MET j 54 " --> pdb=" O SER j 64 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N SER j 64 " --> pdb=" O MET j 54 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2628 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: 2.81 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5760 1.34 - 1.46: 4076 1.46 - 1.58: 7910 1.58 - 1.71: 1 1.71 - 1.83: 146 Bond restraints: 17893 Sorted by residual: bond pdb=" CB PRO G 57 " pdb=" CG PRO G 57 " ideal model delta sigma weight residual 1.492 1.651 -0.159 5.00e-02 4.00e+02 1.01e+01 bond pdb=" N THR j 74 " pdb=" CA THR j 74 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.06e+00 bond pdb=" N GLY A 5 " pdb=" CA GLY A 5 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.21e+00 bond pdb=" N GLY F 5 " pdb=" CA GLY F 5 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.20e+00 bond pdb=" N GLY G 4 " pdb=" CA GLY G 4 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.14e+00 ... (remaining 17888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 24222 2.99 - 5.97: 124 5.97 - 8.96: 5 8.96 - 11.94: 1 11.94 - 14.93: 1 Bond angle restraints: 24353 Sorted by residual: angle pdb=" CA PRO G 57 " pdb=" N PRO G 57 " pdb=" CD PRO G 57 " ideal model delta sigma weight residual 112.00 97.07 14.93 1.40e+00 5.10e-01 1.14e+02 angle pdb=" C GLN B 230 " pdb=" CA GLN B 230 " pdb=" CB GLN B 230 " ideal model delta sigma weight residual 117.23 111.01 6.22 1.36e+00 5.41e-01 2.09e+01 angle pdb=" C LEU j 33 " pdb=" CA LEU j 33 " pdb=" CB LEU j 33 " ideal model delta sigma weight residual 116.63 111.39 5.24 1.16e+00 7.43e-01 2.04e+01 angle pdb=" C LEU A 182 " pdb=" CA LEU A 182 " pdb=" CB LEU A 182 " ideal model delta sigma weight residual 115.79 111.18 4.61 1.19e+00 7.06e-01 1.50e+01 angle pdb=" N PRO G 57 " pdb=" CD PRO G 57 " pdb=" CG PRO G 57 " ideal model delta sigma weight residual 103.20 97.83 5.37 1.50e+00 4.44e-01 1.28e+01 ... (remaining 24348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 9474 17.35 - 34.69: 913 34.69 - 52.04: 224 52.04 - 69.38: 34 69.38 - 86.73: 19 Dihedral angle restraints: 10664 sinusoidal: 3749 harmonic: 6915 Sorted by residual: dihedral pdb=" CB CYS G 115 " pdb=" SG CYS G 115 " pdb=" SG CYS G 154 " pdb=" CB CYS G 154 " ideal model delta sinusoidal sigma weight residual 93.00 147.65 -54.65 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CG ARG E 51 " pdb=" CD ARG E 51 " pdb=" NE ARG E 51 " pdb=" CZ ARG E 51 " ideal model delta sinusoidal sigma weight residual -90.00 -134.90 44.90 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA VAL B 21 " pdb=" C VAL B 21 " pdb=" N GLU B 22 " pdb=" CA GLU B 22 " ideal model delta harmonic sigma weight residual 180.00 164.12 15.88 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 10661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1922 0.030 - 0.060: 596 0.060 - 0.090: 199 0.090 - 0.120: 146 0.120 - 0.150: 18 Chirality restraints: 2881 Sorted by residual: chirality pdb=" CA ILE B 105 " pdb=" N ILE B 105 " pdb=" C ILE B 105 " pdb=" CB ILE B 105 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE c 228 " pdb=" N ILE c 228 " pdb=" C ILE c 228 " pdb=" CB ILE c 228 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE E 223 " pdb=" N ILE E 223 " pdb=" C ILE E 223 " pdb=" CB ILE E 223 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 2878 not shown) Planarity restraints: 3113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 56 " 0.114 5.00e-02 4.00e+02 1.59e-01 4.05e+01 pdb=" N PRO G 57 " -0.275 5.00e-02 4.00e+02 pdb=" CA PRO G 57 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO G 57 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 14 " 0.049 5.00e-02 4.00e+02 7.41e-02 8.78e+00 pdb=" N PRO A 15 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 15 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 15 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 20 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.16e+00 pdb=" C GLN B 20 " -0.049 2.00e-02 2.50e+03 pdb=" O GLN B 20 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL B 21 " 0.017 2.00e-02 2.50e+03 ... (remaining 3110 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 145 2.55 - 3.14: 14678 3.14 - 3.72: 28599 3.72 - 4.31: 39017 4.31 - 4.90: 65470 Nonbonded interactions: 147909 Sorted by model distance: nonbonded pdb=" OG SER i 29 " pdb=" O PRO j 45 " model vdw 1.960 3.040 nonbonded pdb=" O PRO E 15 " pdb=" NZ LYS F 29 " model vdw 2.093 3.120 nonbonded pdb=" OD2 ASP C 139 " pdb=" OG1 THR C 141 " model vdw 2.111 3.040 nonbonded pdb=" O GLN D 114 " pdb=" OG SER D 117 " model vdw 2.124 3.040 nonbonded pdb=" OE1 GLN D 114 " pdb=" NH1 ARG E 82 " model vdw 2.160 3.120 ... (remaining 147904 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.440 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 16.310 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.159 17894 Z= 0.132 Angle : 0.559 14.928 24355 Z= 0.309 Chirality : 0.039 0.150 2881 Planarity : 0.005 0.159 3113 Dihedral : 14.987 86.725 6199 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 0.23 % Allowed : 22.58 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.18), residues: 2351 helix: 1.87 (0.18), residues: 888 sheet: -1.43 (0.24), residues: 487 loop : -1.08 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 218 TYR 0.014 0.001 TYR c 66 PHE 0.015 0.001 PHE d 102 TRP 0.005 0.001 TRP D 100 HIS 0.002 0.001 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.00289 (17893) covalent geometry : angle 0.55875 (24353) SS BOND : bond 0.00158 ( 1) SS BOND : angle 1.66482 ( 2) hydrogen bonds : bond 0.17226 ( 925) hydrogen bonds : angle 7.62338 ( 2628) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 411 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8886 (mmmm) cc_final: 0.8462 (mmmt) REVERT: B 17 ARG cc_start: 0.7423 (mtm110) cc_final: 0.7037 (ptm160) REVERT: B 159 TRP cc_start: 0.7950 (m100) cc_final: 0.7520 (m100) REVERT: C 166 LYS cc_start: 0.8458 (mptt) cc_final: 0.8131 (mppt) REVERT: D 20 ARG cc_start: 0.8553 (mtp180) cc_final: 0.8249 (mmm-85) REVERT: D 29 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8152 (mm-30) REVERT: D 206 MET cc_start: 0.8220 (ttm) cc_final: 0.8002 (ttp) REVERT: E 3 ARG cc_start: 0.8036 (ptm-80) cc_final: 0.7466 (ptm-80) REVERT: E 91 GLU cc_start: 0.8512 (mm-30) cc_final: 0.7756 (mp0) REVERT: G 21 ARG cc_start: 0.8820 (ptm160) cc_final: 0.8529 (ptm-80) REVERT: G 150 GLN cc_start: 0.8511 (mm-40) cc_final: 0.7817 (mt0) REVERT: c 120 PHE cc_start: 0.7558 (p90) cc_final: 0.6978 (p90) REVERT: c 133 PHE cc_start: 0.7497 (m-80) cc_final: 0.6760 (m-80) REVERT: c 163 GLN cc_start: 0.8480 (mp10) cc_final: 0.7700 (mp10) REVERT: c 248 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7599 (tt0) REVERT: d 40 ASN cc_start: 0.9190 (t0) cc_final: 0.8697 (t0) REVERT: d 141 TYR cc_start: 0.7461 (p90) cc_final: 0.7216 (p90) REVERT: d 152 GLN cc_start: 0.7719 (mt0) cc_final: 0.7442 (mp10) REVERT: d 193 GLU cc_start: 0.8456 (tp30) cc_final: 0.8138 (mm-30) REVERT: d 200 GLN cc_start: 0.7817 (mp10) cc_final: 0.7419 (tm-30) REVERT: i 48 LEU cc_start: 0.8408 (mm) cc_final: 0.8089 (mt) outliers start: 4 outliers final: 0 residues processed: 412 average time/residue: 0.5241 time to fit residues: 243.1428 Evaluate side-chains 327 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 ASN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 12 HIS G 53 GLN c 103 ASN c 136 GLN c 283 GLN d 29 GLN d 153 ASN j 46 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.088970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.073929 restraints weight = 50865.691| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.48 r_work: 0.3133 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 17894 Z= 0.338 Angle : 0.760 10.655 24355 Z= 0.402 Chirality : 0.047 0.255 2881 Planarity : 0.006 0.091 3113 Dihedral : 4.726 21.513 2545 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 6.14 % Allowed : 21.31 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.17), residues: 2351 helix: 1.28 (0.17), residues: 896 sheet: -1.58 (0.22), residues: 524 loop : -1.14 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 93 TYR 0.025 0.002 TYR F 123 PHE 0.023 0.003 PHE j 92 TRP 0.018 0.002 TRP j 40 HIS 0.008 0.002 HIS j 27 Details of bonding type rmsd covalent geometry : bond 0.00765 (17893) covalent geometry : angle 0.75972 (24353) SS BOND : bond 0.00157 ( 1) SS BOND : angle 2.04885 ( 2) hydrogen bonds : bond 0.04908 ( 925) hydrogen bonds : angle 5.93388 ( 2628) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 335 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 PHE cc_start: 0.9089 (m-80) cc_final: 0.8796 (m-80) REVERT: A 49 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: A 118 MET cc_start: 0.7789 (mmm) cc_final: 0.7360 (mtm) REVERT: A 163 MET cc_start: 0.8725 (ptp) cc_final: 0.8361 (ptp) REVERT: A 203 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.7845 (mtt) REVERT: B 17 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7393 (ptm160) REVERT: B 57 ASP cc_start: 0.7316 (t0) cc_final: 0.7024 (t0) REVERT: B 89 GLU cc_start: 0.9380 (tp30) cc_final: 0.8640 (tp30) REVERT: C 166 LYS cc_start: 0.8874 (mptt) cc_final: 0.8466 (mppt) REVERT: C 205 ASN cc_start: 0.8929 (m110) cc_final: 0.8263 (p0) REVERT: D 118 ASN cc_start: 0.8479 (m-40) cc_final: 0.8274 (m-40) REVERT: D 189 MET cc_start: 0.8918 (mtp) cc_final: 0.8609 (mtt) REVERT: E 86 ASN cc_start: 0.9404 (m-40) cc_final: 0.9116 (m-40) REVERT: E 226 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.7586 (t70) REVERT: F 144 ASN cc_start: 0.8759 (t0) cc_final: 0.8166 (t0) REVERT: F 182 MET cc_start: 0.8905 (pmm) cc_final: 0.8652 (pmm) REVERT: F 206 LYS cc_start: 0.9348 (mmmm) cc_final: 0.9089 (mmpt) REVERT: G 21 ARG cc_start: 0.9140 (ptm160) cc_final: 0.8852 (mtp-110) REVERT: G 70 PHE cc_start: 0.8403 (m-80) cc_final: 0.8132 (m-80) REVERT: G 93 ARG cc_start: 0.9225 (tpt-90) cc_final: 0.8957 (tpt-90) REVERT: c 133 PHE cc_start: 0.7871 (m-80) cc_final: 0.7074 (m-80) REVERT: c 157 CYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8247 (t) REVERT: c 198 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7735 (pptt) REVERT: c 277 MET cc_start: 0.8650 (mpt) cc_final: 0.8423 (mpt) REVERT: d 152 GLN cc_start: 0.7851 (mt0) cc_final: 0.7498 (mt0) REVERT: d 200 GLN cc_start: 0.8287 (mp10) cc_final: 0.7636 (tm-30) REVERT: i 49 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8093 (tm-30) REVERT: j 59 ASP cc_start: 0.7915 (t0) cc_final: 0.7626 (t0) outliers start: 106 outliers final: 46 residues processed: 402 average time/residue: 0.4654 time to fit residues: 212.0434 Evaluate side-chains 344 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 293 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 161 CYS Chi-restraints excluded: chain c residue 46 GLU Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 157 CYS Chi-restraints excluded: chain c residue 177 THR Chi-restraints excluded: chain c residue 198 LYS Chi-restraints excluded: chain c residue 221 SER Chi-restraints excluded: chain c residue 256 THR Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 51 CYS Chi-restraints excluded: chain d residue 53 VAL Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain i residue 39 PHE Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 74 LEU Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 71 THR Chi-restraints excluded: chain j residue 77 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 195 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 112 optimal weight: 0.0170 chunk 47 optimal weight: 0.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN B 69 ASN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** E 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 HIS c 145 GLN c 283 GLN d 153 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.092587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077473 restraints weight = 49402.464| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.51 r_work: 0.3206 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17894 Z= 0.136 Angle : 0.609 11.045 24355 Z= 0.316 Chirality : 0.043 0.288 2881 Planarity : 0.005 0.068 3113 Dihedral : 4.351 20.668 2545 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 4.52 % Allowed : 24.96 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.18), residues: 2351 helix: 1.64 (0.17), residues: 902 sheet: -1.54 (0.22), residues: 517 loop : -1.00 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG j 57 TYR 0.022 0.001 TYR G 159 PHE 0.017 0.001 PHE j 104 TRP 0.011 0.001 TRP d 109 HIS 0.004 0.001 HIS F 121 Details of bonding type rmsd covalent geometry : bond 0.00312 (17893) covalent geometry : angle 0.60813 (24353) SS BOND : bond 0.00704 ( 1) SS BOND : angle 3.64884 ( 2) hydrogen bonds : bond 0.03604 ( 925) hydrogen bonds : angle 5.28522 ( 2628) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 380 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7652 (m-80) cc_final: 0.6978 (m-80) REVERT: A 7 SER cc_start: 0.7994 (m) cc_final: 0.7649 (p) REVERT: A 92 LYS cc_start: 0.8802 (mmmm) cc_final: 0.8595 (mmmm) REVERT: A 118 MET cc_start: 0.7716 (mmm) cc_final: 0.7400 (mtm) REVERT: A 163 MET cc_start: 0.8832 (ptp) cc_final: 0.8460 (ptp) REVERT: A 173 PHE cc_start: 0.7874 (t80) cc_final: 0.7444 (t80) REVERT: A 189 HIS cc_start: 0.8030 (OUTLIER) cc_final: 0.7674 (m-70) REVERT: B 17 ARG cc_start: 0.7982 (mtm110) cc_final: 0.7427 (ptm160) REVERT: B 57 ASP cc_start: 0.7245 (t0) cc_final: 0.6857 (t0) REVERT: B 139 TRP cc_start: 0.8845 (t60) cc_final: 0.8396 (t60) REVERT: B 149 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8486 (tm-30) REVERT: C 146 GLN cc_start: 0.8772 (tm-30) cc_final: 0.7976 (tm-30) REVERT: C 166 LYS cc_start: 0.8736 (mptt) cc_final: 0.8322 (mppt) REVERT: C 205 ASN cc_start: 0.8852 (m110) cc_final: 0.8177 (p0) REVERT: D 53 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8364 (ptt180) REVERT: D 110 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8430 (tm-30) REVERT: D 189 MET cc_start: 0.8918 (mtp) cc_final: 0.8551 (mtt) REVERT: E 19 ILE cc_start: 0.9109 (mp) cc_final: 0.8753 (mt) REVERT: E 27 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8871 (mm-30) REVERT: E 30 LYS cc_start: 0.9365 (mtmm) cc_final: 0.9162 (mtmt) REVERT: E 61 LYS cc_start: 0.8901 (mttt) cc_final: 0.8485 (mmmt) REVERT: F 206 LYS cc_start: 0.9297 (mmmm) cc_final: 0.9096 (mmpt) REVERT: G 11 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7919 (ptp90) REVERT: G 19 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8516 (mm-30) REVERT: G 21 ARG cc_start: 0.9140 (ptm160) cc_final: 0.8796 (mtp-110) REVERT: G 80 MET cc_start: 0.8527 (mmm) cc_final: 0.8217 (mmm) REVERT: G 88 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8612 (mtm-85) REVERT: G 236 ASP cc_start: 0.8496 (p0) cc_final: 0.8271 (p0) REVERT: c 133 PHE cc_start: 0.7803 (m-80) cc_final: 0.7366 (m-80) REVERT: c 157 CYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8422 (t) REVERT: c 256 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8727 (p) REVERT: c 283 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8196 (pp30) REVERT: c 287 TYR cc_start: 0.9157 (m-80) cc_final: 0.8950 (m-80) REVERT: d 32 MET cc_start: 0.8098 (mmm) cc_final: 0.7764 (mmm) REVERT: d 67 ASN cc_start: 0.9119 (m-40) cc_final: 0.8700 (p0) REVERT: d 141 TYR cc_start: 0.7905 (p90) cc_final: 0.7463 (p90) REVERT: d 152 GLN cc_start: 0.7978 (mt0) cc_final: 0.7642 (mp10) REVERT: d 200 GLN cc_start: 0.8192 (mp10) cc_final: 0.7529 (tm-30) REVERT: d 218 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9114 (mm) REVERT: i 11 GLN cc_start: 0.7663 (tp40) cc_final: 0.7414 (tm-30) REVERT: i 14 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7360 (tm-30) REVERT: j 54 MET cc_start: 0.6819 (ptt) cc_final: 0.6593 (pmm) REVERT: j 59 ASP cc_start: 0.7930 (t0) cc_final: 0.7623 (t0) outliers start: 78 outliers final: 26 residues processed: 427 average time/residue: 0.5506 time to fit residues: 265.0638 Evaluate side-chains 352 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 317 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 137 CYS Chi-restraints excluded: chain c residue 46 GLU Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 157 CYS Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 198 LYS Chi-restraints excluded: chain c residue 256 THR Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 218 LEU Chi-restraints excluded: chain j residue 86 LYS Chi-restraints excluded: chain j residue 113 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 100 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 204 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 220 ASN C 85 ASN D 204 GLN ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN ** c 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 153 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.090045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.074762 restraints weight = 50310.156| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.51 r_work: 0.3151 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17894 Z= 0.223 Angle : 0.653 12.728 24355 Z= 0.342 Chirality : 0.044 0.350 2881 Planarity : 0.005 0.063 3113 Dihedral : 4.442 20.063 2545 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.94 % Rotamer: Outliers : 5.91 % Allowed : 24.38 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.18), residues: 2351 helix: 1.47 (0.17), residues: 901 sheet: -1.52 (0.21), residues: 536 loop : -1.04 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 51 TYR 0.022 0.002 TYR A 167 PHE 0.017 0.002 PHE d 102 TRP 0.013 0.001 TRP d 160 HIS 0.004 0.001 HIS F 121 Details of bonding type rmsd covalent geometry : bond 0.00508 (17893) covalent geometry : angle 0.65240 (24353) SS BOND : bond 0.00442 ( 1) SS BOND : angle 3.23747 ( 2) hydrogen bonds : bond 0.03894 ( 925) hydrogen bonds : angle 5.33596 ( 2628) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 328 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7662 (m-80) cc_final: 0.7168 (m-80) REVERT: A 7 SER cc_start: 0.8074 (m) cc_final: 0.7704 (p) REVERT: A 118 MET cc_start: 0.7663 (mmm) cc_final: 0.7344 (mtm) REVERT: A 163 MET cc_start: 0.8795 (ptp) cc_final: 0.8427 (ptp) REVERT: A 177 ARG cc_start: 0.8730 (ttm-80) cc_final: 0.8381 (ptm160) REVERT: A 189 HIS cc_start: 0.8030 (OUTLIER) cc_final: 0.7714 (m-70) REVERT: B 49 ARG cc_start: 0.8088 (tpp80) cc_final: 0.7693 (ttm110) REVERT: B 57 ASP cc_start: 0.7432 (t0) cc_final: 0.6995 (t0) REVERT: B 139 TRP cc_start: 0.8817 (t60) cc_final: 0.8447 (t60) REVERT: B 149 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8461 (tm-30) REVERT: B 184 MET cc_start: 0.6457 (OUTLIER) cc_final: 0.5353 (ptp) REVERT: C 166 LYS cc_start: 0.8824 (mptt) cc_final: 0.8356 (mppt) REVERT: C 205 ASN cc_start: 0.8988 (m110) cc_final: 0.8270 (p0) REVERT: D 53 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8350 (ptt180) REVERT: D 110 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8518 (tm-30) REVERT: D 174 SER cc_start: 0.9117 (m) cc_final: 0.8757 (t) REVERT: D 189 MET cc_start: 0.8920 (mtp) cc_final: 0.8560 (mtt) REVERT: E 19 ILE cc_start: 0.9196 (mp) cc_final: 0.8849 (mt) REVERT: E 61 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8644 (mmmt) REVERT: E 91 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8402 (mp0) REVERT: E 226 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.7474 (t70) REVERT: G 11 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7833 (ptp90) REVERT: G 19 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8508 (mm-30) REVERT: G 21 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8910 (mtp-110) REVERT: G 80 MET cc_start: 0.8614 (mmm) cc_final: 0.8405 (mmm) REVERT: G 88 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8662 (mtm-85) REVERT: G 236 ASP cc_start: 0.8515 (p0) cc_final: 0.8269 (p0) REVERT: c 120 PHE cc_start: 0.7686 (p90) cc_final: 0.7067 (p90) REVERT: c 133 PHE cc_start: 0.7812 (m-80) cc_final: 0.7443 (m-80) REVERT: c 157 CYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8443 (t) REVERT: c 202 CYS cc_start: 0.8698 (p) cc_final: 0.8495 (p) REVERT: c 256 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8620 (p) REVERT: d 67 ASN cc_start: 0.9102 (m-40) cc_final: 0.8669 (p0) REVERT: d 141 TYR cc_start: 0.7932 (p90) cc_final: 0.7566 (p90) REVERT: d 152 GLN cc_start: 0.7994 (mt0) cc_final: 0.7648 (mp10) REVERT: d 200 GLN cc_start: 0.8210 (mp10) cc_final: 0.7686 (tm-30) REVERT: d 218 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9097 (mm) REVERT: i 14 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7131 (tm-30) REVERT: j 54 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6886 (ptp) REVERT: j 59 ASP cc_start: 0.8187 (t0) cc_final: 0.7858 (t0) outliers start: 102 outliers final: 51 residues processed: 389 average time/residue: 0.5617 time to fit residues: 246.9091 Evaluate side-chains 364 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 300 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 157 CYS Chi-restraints excluded: chain c residue 162 MET Chi-restraints excluded: chain c residue 169 CYS Chi-restraints excluded: chain c residue 198 LYS Chi-restraints excluded: chain c residue 256 THR Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 51 CYS Chi-restraints excluded: chain d residue 52 LEU Chi-restraints excluded: chain d residue 53 VAL Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain d residue 218 LEU Chi-restraints excluded: chain i residue 39 PHE Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 74 LEU Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 54 MET Chi-restraints excluded: chain j residue 71 THR Chi-restraints excluded: chain j residue 77 THR Chi-restraints excluded: chain j residue 86 LYS Chi-restraints excluded: chain j residue 113 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 199 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 114 optimal weight: 0.0870 chunk 139 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 chunk 98 optimal weight: 0.0170 chunk 89 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 211 optimal weight: 0.0980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 220 ASN E 90 GLN F 121 HIS c 283 GLN d 153 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.093658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.078604 restraints weight = 48936.131| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.51 r_work: 0.3210 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17894 Z= 0.122 Angle : 0.609 12.885 24355 Z= 0.315 Chirality : 0.043 0.340 2881 Planarity : 0.005 0.060 3113 Dihedral : 4.264 20.549 2545 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 4.11 % Allowed : 26.87 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.18), residues: 2351 helix: 1.67 (0.18), residues: 894 sheet: -1.42 (0.22), residues: 508 loop : -0.89 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG j 57 TYR 0.024 0.001 TYR A 167 PHE 0.017 0.001 PHE E 221 TRP 0.018 0.001 TRP d 160 HIS 0.004 0.001 HIS i 31 Details of bonding type rmsd covalent geometry : bond 0.00282 (17893) covalent geometry : angle 0.60826 (24353) SS BOND : bond 0.00333 ( 1) SS BOND : angle 2.66278 ( 2) hydrogen bonds : bond 0.03203 ( 925) hydrogen bonds : angle 4.92566 ( 2628) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 372 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7761 (m-80) cc_final: 0.7281 (m-80) REVERT: A 7 SER cc_start: 0.8080 (m) cc_final: 0.7880 (p) REVERT: A 50 LYS cc_start: 0.6899 (tptp) cc_final: 0.6172 (tptp) REVERT: A 92 LYS cc_start: 0.8372 (mmmm) cc_final: 0.8063 (mmmt) REVERT: A 163 MET cc_start: 0.8733 (ptp) cc_final: 0.8273 (ptp) REVERT: A 177 ARG cc_start: 0.8695 (ttm-80) cc_final: 0.8449 (ptm-80) REVERT: B 49 ARG cc_start: 0.8068 (tpp80) cc_final: 0.7721 (ttm110) REVERT: B 57 ASP cc_start: 0.7396 (t0) cc_final: 0.7006 (t0) REVERT: B 139 TRP cc_start: 0.8835 (t60) cc_final: 0.8356 (t60) REVERT: B 149 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8164 (tm-30) REVERT: B 184 MET cc_start: 0.6244 (OUTLIER) cc_final: 0.5058 (ptp) REVERT: C 85 ASN cc_start: 0.8908 (m-40) cc_final: 0.8647 (m110) REVERT: C 146 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8111 (tm-30) REVERT: C 166 LYS cc_start: 0.8727 (mptt) cc_final: 0.8226 (mppt) REVERT: C 205 ASN cc_start: 0.8863 (m110) cc_final: 0.8145 (p0) REVERT: D 29 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8385 (mm-30) REVERT: D 189 MET cc_start: 0.8922 (mtp) cc_final: 0.8496 (mtt) REVERT: E 19 ILE cc_start: 0.9074 (mp) cc_final: 0.8710 (mt) REVERT: E 61 LYS cc_start: 0.8933 (mttt) cc_final: 0.8550 (mmmt) REVERT: F 182 MET cc_start: 0.8981 (pmm) cc_final: 0.8481 (pmm) REVERT: G 19 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8578 (mm-30) REVERT: G 21 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8724 (mtp-110) REVERT: G 80 MET cc_start: 0.8519 (mmm) cc_final: 0.8297 (mmm) REVERT: G 236 ASP cc_start: 0.8499 (p0) cc_final: 0.8231 (p0) REVERT: c 46 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6631 (pm20) REVERT: c 120 PHE cc_start: 0.7741 (p90) cc_final: 0.7077 (p90) REVERT: c 123 PHE cc_start: 0.7954 (m-80) cc_final: 0.6939 (m-80) REVERT: c 133 PHE cc_start: 0.7783 (m-80) cc_final: 0.7464 (m-80) REVERT: c 157 CYS cc_start: 0.8775 (m) cc_final: 0.8415 (t) REVERT: c 256 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8791 (p) REVERT: d 40 ASN cc_start: 0.9383 (t0) cc_final: 0.8971 (t0) REVERT: d 67 ASN cc_start: 0.9084 (m-40) cc_final: 0.8642 (p0) REVERT: d 141 TYR cc_start: 0.7796 (p90) cc_final: 0.7409 (p90) REVERT: d 152 GLN cc_start: 0.8058 (mt0) cc_final: 0.7727 (mp10) REVERT: d 200 GLN cc_start: 0.8074 (mp10) cc_final: 0.7501 (tm-30) REVERT: j 59 ASP cc_start: 0.8196 (t0) cc_final: 0.7868 (t0) outliers start: 71 outliers final: 34 residues processed: 410 average time/residue: 0.4925 time to fit residues: 228.3213 Evaluate side-chains 359 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 321 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 2 PHE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 256 THR Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 86 LYS Chi-restraints excluded: chain j residue 113 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 41 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 228 optimal weight: 0.3980 chunk 136 optimal weight: 2.9990 chunk 219 optimal weight: 0.7980 chunk 189 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN D 118 ASN E 5 GLN ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 203 GLN c 283 GLN d 153 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.090745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.075902 restraints weight = 49551.195| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.45 r_work: 0.3172 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17894 Z= 0.192 Angle : 0.647 13.200 24355 Z= 0.336 Chirality : 0.044 0.364 2881 Planarity : 0.005 0.068 3113 Dihedral : 4.332 19.862 2545 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.93 % Favored : 94.98 % Rotamer: Outliers : 5.33 % Allowed : 27.27 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.18), residues: 2351 helix: 1.63 (0.18), residues: 903 sheet: -1.43 (0.22), residues: 524 loop : -0.91 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG j 57 TYR 0.028 0.002 TYR A 76 PHE 0.020 0.002 PHE j 104 TRP 0.017 0.001 TRP d 160 HIS 0.003 0.001 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00444 (17893) covalent geometry : angle 0.64705 (24353) SS BOND : bond 0.00513 ( 1) SS BOND : angle 2.50446 ( 2) hydrogen bonds : bond 0.03610 ( 925) hydrogen bonds : angle 5.05514 ( 2628) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 322 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7939 (m-80) cc_final: 0.7550 (m-80) REVERT: A 50 LYS cc_start: 0.7057 (tptp) cc_final: 0.6365 (tptp) REVERT: A 163 MET cc_start: 0.8718 (ptp) cc_final: 0.8336 (ptp) REVERT: A 177 ARG cc_start: 0.8657 (ttm-80) cc_final: 0.8453 (ptm-80) REVERT: A 189 HIS cc_start: 0.8025 (OUTLIER) cc_final: 0.7811 (m-70) REVERT: B 49 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7735 (tpp80) REVERT: B 57 ASP cc_start: 0.7498 (t0) cc_final: 0.7114 (t0) REVERT: B 139 TRP cc_start: 0.8857 (t60) cc_final: 0.8397 (t60) REVERT: B 149 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8421 (tm-30) REVERT: B 184 MET cc_start: 0.6204 (OUTLIER) cc_final: 0.5219 (ptp) REVERT: C 166 LYS cc_start: 0.8799 (mptt) cc_final: 0.8314 (mppt) REVERT: C 205 ASN cc_start: 0.8966 (m110) cc_final: 0.8281 (p0) REVERT: D 53 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8458 (ptt180) REVERT: D 118 ASN cc_start: 0.8651 (m-40) cc_final: 0.8345 (m110) REVERT: D 174 SER cc_start: 0.9109 (m) cc_final: 0.8774 (t) REVERT: E 61 LYS cc_start: 0.8949 (mttt) cc_final: 0.8571 (mmmt) REVERT: E 91 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8267 (mp0) REVERT: E 226 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.7484 (t70) REVERT: F 28 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.7962 (mmm) REVERT: F 182 MET cc_start: 0.8994 (pmm) cc_final: 0.8477 (pmm) REVERT: G 19 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8562 (mm-30) REVERT: G 21 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8806 (mtp-110) REVERT: G 236 ASP cc_start: 0.8494 (p0) cc_final: 0.8240 (p0) REVERT: c 120 PHE cc_start: 0.7747 (p90) cc_final: 0.7084 (p90) REVERT: c 123 PHE cc_start: 0.8032 (m-80) cc_final: 0.7019 (m-80) REVERT: c 133 PHE cc_start: 0.7803 (m-80) cc_final: 0.7470 (m-80) REVERT: c 157 CYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8449 (t) REVERT: c 251 LYS cc_start: 0.8753 (ttmm) cc_final: 0.8208 (tmmt) REVERT: c 256 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8786 (p) REVERT: c 277 MET cc_start: 0.8247 (mpt) cc_final: 0.8024 (mpt) REVERT: d 40 ASN cc_start: 0.9398 (t0) cc_final: 0.8937 (t0) REVERT: d 67 ASN cc_start: 0.9105 (m-40) cc_final: 0.8676 (p0) REVERT: d 141 TYR cc_start: 0.7915 (p90) cc_final: 0.7603 (p90) REVERT: d 152 GLN cc_start: 0.8080 (mt0) cc_final: 0.7827 (mp10) REVERT: d 200 GLN cc_start: 0.8168 (mp10) cc_final: 0.7738 (tm-30) REVERT: j 59 ASP cc_start: 0.8225 (t0) cc_final: 0.7913 (t0) outliers start: 92 outliers final: 50 residues processed: 379 average time/residue: 0.4965 time to fit residues: 212.7621 Evaluate side-chains 363 residues out of total 2044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 304 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain D residue 2 PHE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain F residue 28 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 157 CYS Chi-restraints excluded: chain c residue 169 CYS Chi-restraints excluded: chain c residue 198 LYS Chi-restraints excluded: chain c residue 256 THR Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 51 CYS Chi-restraints excluded: chain d residue 53 VAL Chi-restraints excluded: chain d residue 61 TYR Chi-restraints excluded: chain d residue 189 THR Chi-restraints excluded: chain i residue 39 PHE Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 86 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.3572 > 50: distance: 103 - 108: 10.097 distance: 108 - 109: 14.185 distance: 109 - 110: 24.602 distance: 109 - 112: 17.814 distance: 110 - 111: 28.111 distance: 110 - 116: 8.949 distance: 112 - 113: 5.060 distance: 113 - 115: 32.863 distance: 116 - 117: 15.406 distance: 117 - 118: 24.413 distance: 117 - 120: 24.228 distance: 118 - 119: 25.412 distance: 118 - 121: 16.874 distance: 121 - 122: 42.880 distance: 122 - 123: 10.772 distance: 123 - 124: 6.841 distance: 123 - 125: 9.500 distance: 125 - 126: 8.184 distance: 126 - 127: 11.971 distance: 126 - 129: 14.561 distance: 127 - 128: 8.431 distance: 127 - 131: 14.840 distance: 129 - 130: 4.797 distance: 132 - 133: 23.451 distance: 133 - 134: 19.840 distance: 133 - 135: 19.844 distance: 135 - 136: 3.942 distance: 136 - 137: 8.665 distance: 136 - 139: 19.353 distance: 137 - 138: 15.141 distance: 137 - 143: 23.402 distance: 140 - 141: 22.681 distance: 140 - 142: 33.340 distance: 143 - 144: 11.578 distance: 143 - 149: 35.602 distance: 144 - 145: 8.051 distance: 144 - 147: 13.577 distance: 145 - 146: 34.953 distance: 145 - 150: 11.083 distance: 147 - 148: 40.629 distance: 148 - 149: 19.927 distance: 150 - 151: 5.812 distance: 150 - 156: 13.308 distance: 151 - 152: 30.276 distance: 151 - 154: 20.010 distance: 152 - 153: 20.434 distance: 152 - 157: 15.444 distance: 154 - 155: 10.872 distance: 155 - 156: 17.328 distance: 158 - 159: 7.625 distance: 158 - 161: 8.435 distance: 159 - 160: 9.350 distance: 159 - 162: 4.649 distance: 162 - 163: 3.693 distance: 163 - 164: 4.328 distance: 163 - 166: 3.163 distance: 166 - 167: 4.909 distance: 167 - 169: 3.857